Haruhi Suzumiya/WMG/Mikuru Asahina

Mikuru is the daughter of Kyon's sister and haruhi's brother
This would explain why mikuru acts and looks a lot like his siter but yet have a couple similarities to haruhi. i doubt that she's kyon and haruhi's daughter though since she doesn't treat them like they are her parents.

Mikuru is really Kyon's sister via Time Travel.
This theory comes from the fact that both of them did a "knock on their head and stick out their tongue" gesture. They also share the same eye color and have similar facial structures; Kyon's sister's hair is a couple shades darker than Mikuru's, but Mikuru could have artificially lightened it in order to minimize her resemblance to her younger self. Mikuru also is remarkably at ease around Kyon, to the point of roughhousing and horseplay (if Haruhi isn't around), which seems to be quite at odds with her otherwise timid nature. She also suggests more than once that Kyon should not become "interested" in her. "Book 2: "I was so exhausted already. The thoughts of becoming a voyeur cameraman had long evaporated from my head. Of course, it would be a different story if it involved Asahina-san, but I'm not that sick as to want to preserve video images of my own sister!" Book 3, Bamboo Leaf Rhapsody, lying about Mikuru: "That's my sister." Book 5, when looking at Mikoru: "It felt as if I were looking at my sister in yukata, aside from the overly voluptuous bust." Book 5, Snowy Mountain Syndrome: "Having my sister in my room... As if I would do anything to her. I might go down the slippery slope if I am to share a room with Asahina-san. Whether it'd be my sister or Shamisen is really of no difference to me." Book 6: "Asahina-san's tiny footsteps, coupled with her childlike features, made me wonder, was she really a year older than me? Her footsteps could easily compare to my sister's" Book 7, on reaction to puppies: "If possible, I would like to bring Asahina-san here one day. I could picture her picking up one of those adorable puppies, her eyes sparkling in the process, as she made a shout of “Kyaa~”. That was something I had seen my sister do before, and I had no doubt Asahina-san would be the same.""
 * This theory, unfortunately, is undermined by the vast difference in personalities. Kyon's little sister is, to put it mildly, a little fireball. Unless she suffered some dramatic trauma, it seems unlikely that she would grow up into the pathologically timid Mikuru.
 * A variation that accounts for this is that Mikuru is Kyon's sister from an Alternate Universe where Kyon died. Possibly, the presence of Haruhi has prevented it in this timeline; also possibly, she's going to cause it.
 * Actually, this theory works as is if we combine it with the "Mikuru isn't really as innocent as she seems." theory.
 * Or maybe not. When first dressed as a bunny girl, Mikuru said to Kyon "If I become spoiled for marriage, would you take me?". This doesn't sound like something she'd say to her brother!
 * Someone with an old-fashioned (and by that I mean almost feudal) and sexually innocent view of the world might. Incest Is Relative after all. (Okay, I just love that trope name).
 * The shared gesture can also be explained by the fact that Mikuru and Kyon's sister have spent some time together on several occasions and Kyon's sister could presumably have picked it up off Mikuru, children being impressionable and all. In fact, if I recall correctly it's adult Mikuru that uses the gesture and not young Mikuru, so it's entirely possible that Mikuru actually picked it up off of Imouto.
 * I too noticed the specificity of the gesture and wondered if it meant something, but I think this plays better if Mikuru is Kyon's niece (Imouto's daughter), or maybe a slightly more distant relation along those lines. For something concrete, in one of the short stories Kyon and Mikuru save an elementary-school kid who's apparently crucial to the future development of time travel - it'd be nice to give him time to grow up.
 * The shared gesture is fairly common, actually, not something specific to Mikuru. For another example, see Chiri's disturbing variation, when she tries to become a Dojikko. There are lots more, but that was the first that came to mind.
 * Objection: Doesn't Mikuru make mention of her childhood several times? In the novels, she mentions the stuff they learn in elementary school, she's unaware the ocean's salty, and doesn't understand how boats float. Most of all, when Kyon asks if she would like to stay in the present, she replies that as much as she loves the present (her past), she will only feel most at home in the future (her present). I now invite all the "Lost Twin Sister" and "Time Divergent Entity" Theories.
 * Counter Objection: How is Mikuru's lackluster education relevant as to whether she is Kyon's sister? And besides, her "present" is our future, ergo, Kyon's sister's future. Which is better for you: 2008 or 1998?
 * While I do not believe this myself, I kind of hope it is true because it would be a HILARIOUS kick in the balls for Kyon! I mean, really, can you imagine?
 * Kyon (unwillingly) gropes Mikuru; of course it would be hil-LAR-ious
 * The realization that Haruhi was practically molesting one of his family members, the realization that he'd been unknowingly lusting over his sister the entire time, and the realization that she knew the entire time and never bothered to tell him would hit Kyon with so much shock, embarrassment, and rage at the same time, his reaction would be priceless.
 * I think, this is true. The two share many simmilarities and even look similar. I even think that Kyon mentioned once, that something Mikuru did reminded him on his sister. Also, she also call him by his nickname, even though she is very gentle and polite. Her only reason to call him "Kyon" would be, that she's used to do it, and that would only be the case, if she really was his sister, the very one person, who started the "Kyon-terror". It would a pretty funny slap in the face. Kyon lusted for his annoying, little sister. All the time.
 * This makes so much sense! Now that I think about it, he had multiple comments about not being interested in his sister that way, that is kind of a Suspiciously Specific Denial, in some of these cases he explicitly compared her to Mikuru, claiming that he DOESN'T feel the same way for the two of them. The different personalities and the weird lack of knowledge could be easily explained as the result of the combination of brainwashing by [classified information], and the trauma of constantly getting "raped" by Haruhi, while HER BROTHER watches, and fantasizes about her.
 * The difference in personality wouldn't even require that much, it could be just a result of growing up, people change quite a bit in their teens and she could simply have gone from outgoing and hyper to shy and fragile. Plus, though it's already been stated, Kyon's sister and Mikuru's facial features are, not just similar, but nearly identical.
 * Here is a collection of these comments:

Mikuru is Kyon and Haruhi's future descendant
Make's more sense than his sister, and provides even MORE black humor.
 * Actually it's not farfetched if you think about it. Just take a guess of how far is Mikuru's time (Hint: she can use complex tools for her time -her TPDD and comm device- but doesn't know how to use a computer, so computers aren't common technology anymore). After a few hundred thousand years the whole current cast (except Mukuru) can be ancestor of the people in Mikuru's time. And for that Haruhi's child and Kyon's child don't even have to be the same person.

Mikuru is close to thirty-five years old.
Adult Mikuru is around a hundred.
 * Makes sense, when asked her age is "classified" and many think people will live longer in the future.

Mikuru is, in fact, merely acting weak and helpless in order to get Kyon on her side.
Itsuki explicitly theorizes this at one point. Kyon may not have actual god-like powers on his own, but he may have another, more subtle power which allows him to not only encounter plenty of other Haruhi-esque god-like beings, but also to influence them in a decisive manner. Mikuru is thus able to control the one who controls the gods. This, admittedly, relies a lot on random chance.
 * Or perhaps Mikuru really is that helpless, but she was selected by her superiors for those qualities, in order to appeal to Kyon for much the same reasons.
 * At one point Koizumi outright tells this to Kyon (Near the end of book 2) "Her role is to ensnare you. That's why she looks like that, and that's why she acts like that: a cute, weak-willed girl, the type you'd probably like. You are the only one who can make Haruhi do anything to any degree at all, thus, the best move for her is to entrap you."
 * I find it deeply suspicious that although Itsuki has promised that he would.
 * Except that
 * I think that everyone in the SOS is playing at something similar and will eventually betray Kyon somehow.
 * Possible support for this theory: In book 2 Kyon said that Mikuru would make a better fairy than a Time Traveler. Faeires, aka The Fair Folk, have been known for using their beauty to lure knights into a forest to their death. Foreshadowing much?

Mikuru's spaciness is because of her memory intentionally being "swiss-cheesed" to prevent paradox.
She's the tool of the Future to change the Past. Having her memory change with each change would cause undue stress, so she's intentionally "dumbed down." Note her future self, who is also her Superior, doesn't have this problem in the slightest.
 * Which would reinforce the "Mikuru is Kyon's sister" theory. If she remembered her childhood, she'd give a lot of hints about her identity, and it wouldn't be good for her mission. That Elementary School boy they saved was, in fact, Fujiwara.
 * Jossed. She admits to being conditioned to the point that she physically couldn't say anything she's not supposed to, but at least once in the novels some information gets declassified; Mikuru is actually surprised she can answer the question, but she clearly knew it all along. Also, Future Mikuru comments on how disturbing it is to go back to the past and see all the little differences from how she remembered it; apparently, the entire organisation has Ripple-Effect-Proof Memory.

Mikuru isn't really as innocent as she seems.
Think about it. Nobody can possibly be that shy involuntarily. This is supported by Adult Mikuru's feelings of nostalgia at the costumes into which she was forced; wouldn't she normally be terrified?
 * Someone who is normally that shy would like to dispute this. And nostalgia can cover up a lot. It's perfectly plausible that with a few years of experience, looking back on something that was unpleasant at the time could at least be looked on passively or with humor (as Mikuru seems to). Note that this doesn't contradict the letter of the guess, just the reasoning.
 * Someone who says "You are not cleared for that" that often can't possibly be innocent...
 * It doesn't help that her superiors apparently have her head wired so that they can edit what she can and can't reveal in real time. At least once she was surprised to discover just where the "classified" line was and that it had been moved when she wasn't looking.
 * Also, the only outfit she seemed to have significant issues with was the bunny costume. She seemed to enjoy the others, at least when Haruhi wasn't excitedly "helping" her to change outfits.
 * Alternatively, young Mikuru is good, not knowing what her superior's AKA her Older Self's plans are, and is just an unwitting pawn. Or, alternatively, they're not really the same but clones of the same person (which would make sense, from a crapsack future, cyperpunk kind of view).

== Asahina (Big) is actually from the same time period as Asahina (Small) because Asahina (Small) decided to stay in the past with the SOS Brigade and thus took The Long Way back to her time period. == Think about it... The future inventor of time travel lives near Haruhi, and would likely know who Asahina is. He will likely ask Asahina in the future to help him form the time travel agency, and Asahina will arrange her younger self to be recruited and send her back in time to join the SOS Brigade.

Mikuru is in love with Haruhi
Alas, Kyon's love is to forever go unrequited. Miss Asahina (big) didn't refuse Kyon's kiss because she didn't want to endanger the universe by way of Haruhi's jealousy. It's because she's just not into that. Apparently, all those "cosplay sessions" had an effect on her. The penultimate proof is in the above reference to Snow Mountain Syndrome, in which all the other characters have the objects of their affection show up in their rooms to seduce them, while Haruhi shows up in Mikuru's room.
 * Or Mikuru isn't dumb enough to say it was Kyon and piss off Haruhi. Think what happened when they were just flirting a little too much for Haruhi's liking, now ramp that up a couple notches and probably cut Kyon out of restructuring the world this time. Though it might be interesting as to what he'd have to do this time to get her to come back.
 * Of course, that pokes a few holes in the puzzle involving the doppelgangers. If it was Kyon that Mikuru saw, then the solution used flat out wouldn't have worked.
 * Alternately, Mikuru has always been a lesbian, and Haruhi's actions had no effect on her. Consider that Mikuru only joins the Brigade, in the anime at least, after she notices Yuki, the only girl currently in the Brigade except for Haruhi.
 * On the other hand, it's reasonable to assume that time-travelers would know who the aliens are. Mikuru joining the SOS-dan only after noticing Yuki could be an attempt to learn more about the IDTE.
 * Note who it really is, that Mikuru is lovestruck by in the tenth novel...

Asahina is Drugging Kyon
Kyon is constantly gushing over how everything she makes tastes divine, however, in several places (At the pool, etc) he mentions that he can't actually taste the food, but finds it divine regardless. This is because Mikuru is lacing his portions with LSD. She knows which ones Kyon will choose because Big Mikuru gave her a list. This is why Kyon's such an unreliable narrator, he honestly can't tell between what he's thinking and what he's saying, or even if he said anything at all. this is all a ploy to prevent him from realising his status as mentioned in any given WMG above.
 * Interestingly, He Kyon didn't become such an unreliable narrator until after the first book, that is to say, until after he'd been eating Mikuru's food for some time. (Although it might just be an error with the translation I read.)

Future Mikuru is not current Mikuru.
In the anime, anyway, do we have any proof that she isn't just a body duplicate? They could have gotten hold of Mikuru's body (alive, on their side, both, or neither) and copied it, then gave future Mikuru everything they knew about the original Mikuru's time with Kyon. (For that matter, the original Mikuru may not be any more of a "real" human than future Mikuru, or even Yuki and Asakura.) She just picked something at random about herself that seemed sufficiently intimate. If Kyon had already seen the mole, it would "prove" it was her. If he hadn't, he would be curious enough to ask Mikuru about it, future Mikuru having successfully Tricked-Out Time.
 * Or perhaps she's an alternate future Mikuru. She does mention that Kyon will have to make "The Decision that determines everything" soon.

Mikuru's entire "organization" actually consists of herself
...from various times. This is the real reason she keeps so secretive about her party (unlike Itsuki and Nagato): not to prevent some kind of paradox or anything but to prevent everyone from discovering the fact that she is the only human time-traveler in the past and future.
 * Or, she is her entire organization and doesn't know it. She doesn't know her superior is herself and all of her other memories are suppressed or "classified". For all we know older Mikuru could be running everything with just one time machine. We know that kid who invents time travel doesn't specifically work for her organization since other people have the technology, so Mikuru could have just picked it up at one point, possibly from her future self. And that's assuming the organization is a two-person group, and not hundreds of Mikurus running around.
 * Or, she is her entire organization and doesn't know it. She doesn't know her superior is herself and all of her other memories are suppressed or "classified". For all we know older Mikuru could be running everything with just one time machine. We know that kid who invents time travel doesn't specifically work for her organization since other people have the technology, so Mikuru could have just picked it up at one point, possibly from her future self. And that's assuming the organization is a two-person group, and not hundreds of Mikurus running around.

Mikuru's storybook is a horrible portent of things to come.
Since Kyon and Nagato's stories were based on true events, there's no reason to think Mikuru's isn't either. Discounting the Snow White bits, Mikuru is telling the story of how Haruhi rose to take over the world. First she took control of Koizumi (the Tactician) group's resources. Then, with her the Seven Dwarves (her slowly expanding SOS army) she swarmed over the planet, achieving victory in every battle. Eventually she took over the world and retired somewhere with Kyon, leaving the planet in Koizumi's hands. Mikuru knows all of this, because it is mandatory in the SOS Brigade schools that run all education on the planet.

The only "proof" Mikuru has as to what she needs to do and her importance in the series is her own word, based on her own word, based on her own word...
If Mikuru hadn't been here, everything would have turned out fine, though Tsuruya joining the Haruhi-tachi earlier would have resulted in more of a rough start to the SOS Brigade as she clashed with Haruhi. As it is, her presence settled before it even happened into a pattern that fed into itself to create a timeline where she would travel back in time to follow her own instructions. Yuki and Itsuki would have had the situation well in hand, along with Kyon, with all of the Mikuru-related things (including Bamboo Leaf Rhapsody) having either happened in a much more subdued way, or not happened at all.

In Mikuru's time, human's don't live on Earth.
At some point, Earth will be rendered inhabitable. However, scientists saw it coming, and evacuated all humans to... Mars, or something, with enough supplies of oxygen, food and water to last several thousand years. This is why Mikuru doesn't seem to know anything about water whatsoever.
 * And Chao Lingshen is her best friend or Odd Couple roomate, who inexplicably used outdated spells based on Latin instead of Microsoft SQL? I want this to be true so much.

Anonymous is Mikuru's superior
That is why Mikuru won't reveal anything about her superior, and it is the reason why Mikuru is such a Fanservice Girl.

Yuki and Itsuki are Mikuru' direct superiors.
Yuki and Itsuki are actually more authoritarian, and they know about Haruhi, so they implanted Mikuru in order to study moe's effect on a sociopathic Jerkass Physical God.
 * Itsuki is almost always the odd man out while Yuki and adult Mikuru coordinate closely. What were they protecting by having a Kyon available in "cold storage" for three years? A lot of Mikuru's unease around Yuki can be explained if she knows that Yuki is the big boss and she's just an intern. Note for example how she instantly recognized Yuki when she saw her for the "first" time.

Tsuruya is Mikuru's direct superior.
If an organization of time travelers was willing to employ a 15-year-old girl, they'd probably have more than one. This explains why they're friends even though they're extremely different (particularly in outgoingness - Mikuru is very shy, while Tsuruya is the exact opposite), and also why Tsuruya seems to have had an idea of what was going on for a while. This particular WMG is inspired by a very short shot from the second season, with Tsuruya looking sinister in the shadows in the background while Mikuru tells Kyon that she doesn't agree with Itsuki's theories on Haruhi.
 * Mikuru is 17 or 18. Probably. She's in her final year, anyway. The text for that scene in the novel also portrayed it a little differently: Tsuruya was treating it more like Mikuru was flirting/confessing and was merely a short distance out of hearing range rather than lurking.

Mikuru is Kyon and Haruhi's daughter
Time travel is never Exactly What It Says on the Tin, and Mikuru constantly gives mixed signals between her younger and adult selves. Young Mikuru is attracted to Kyon while Older Mikuru says she can't fall in love with him. It's a more extreme version of when a little girl says she wants to marry her daddy when she grows up, because due to time travel, Mikuru and her father are now the same age and he has all the qualities at this age that make him Mikuru's childhood fantasy. However, young Mikuru did this without telling her parents, thus explaining Older Mikuru appears briefly to tell Kyon exactly what he needs to hear in order to make him vaguely question if pursuing Mikuru is the right thing to do rather than acting on his Tsundere-ish relationship with Haruhi. The implication that Mikuru will have to leave him behind eventually is a pre-warning about the fact that eventually she'll go back to her own time, drifting out of Haruhi and Kyon's life as they get together. Eventually, when they have a red-headed baby girl, Haruhi will decide to name her after Mikuru after their childhood friend who moved away, and a few decades down the line, Kyon will finally noticed that Mikuru grew up to look like...Mikuru...and everyone will have quite the laugh over it all. Similarly, Haruhi's cosplay-rape tendencies that she honed on Mikuru will be repeated on her young daughter, then Haruhi sent Mikuru back in time, thus explaining why, despite her protests(because she's embarassed of being seen naked by a guy), Mikuru's pretty much used to it within an episode of her first appearance: she was raised that way.

Haruhi already knew Mikuru is her daughter from the future
And that is why she keeps manipulating Mikuru with almost absolute freedom. For the classified information thing...... it was only intended for other people besides Haruhi.

Kyon's sister is Mikuru's mom
At some point in the future when she's all done with high school, Kyon's sister will marry someone with the family name Asahina and together they will have a daughter that they will decide to name Mikuru.

Mikuru isn't Japanese.
She has red hair, and when looking at those yukata she said "So this is the traditional wardrobe of this country."
 * She's a (human) Martian, see above.
 * She's also able to read english well enough to aknowlage her name in english. (Meloncoly VI)

Mikuru is a Celestial
Itsuki and Kyon are the actual Time Travellers, and their "dimensional slider" abilities can also allow them to slide back and forth the timeline. The Celestials are in fact humans in the distant future, mutated by Haruhi's desire to express her anger. We all know how Haruhi expresses her anger: by raping Mikuru. (Yuki being a celestial is invalid since she isn't a result of Haruhi's angst). Celestials, being eldritch abominations who share Haruhi's ability of rewriting reality, can disguise themselves as being humans, and being the primal result of Haruhi's desire of being a dominatrix and having a Chew Toy, time-travelled back to the past just to please Haruhi while disguising it as the order of a classified information superior, who is of course... Haruhi. Also, maybe the reason why Itsuki defeats Celestials and prevents them from escaping Closed Space is to keep the celestials from ever going back in time and induce a sense of superiority in Haruhi, which means more controllability for Itsuki and Kyon.
 * Considering Celestials are the AU equivalents of Neon Genesis Evangelion angels, maybe that's the reason why Mikuru stands out as the most beautiful of them all, being an angel....
 * And Kyon is The Doctor, being the actual Time Traveller with the name "John Smith".
 * Wait... how come Mikuru and Itsuki get together well?
 * She got crap past the radar. Itsuki can fight celestials, but can't tell the difference between them and a human.

Mikuru is
First, Haruhi-chan. Second, there is the possibility that Mikuru is Kyon and Haruhi's daughter. For a more biblical explanation: Haruhi seems to represent Judaism and the Old Testament, with a long history of esoteric magic, melancholy, and manipulation of people. Kyon, on the other hand, represents the New Testament, the Roman Empire (he's the majority and was responsible for the spread of Haruhiism), and modern day Christianity (it's the current definition of "normal") with the universalization of old doctrines (Haruhi) and the spread to more "normal" people. However, it is Mikuru, not Kyon, is Jesus (Kyon might be God of the New Testament, but is not Jesus). With Haruhi as the past, Mikuru represents the future (she's a time traveller after all) of Haruhiism (Kyon). She also suffers for Haruhi's sins (which parallels Jesus suffering for the Jews / OT God's sins). Kyon, being the new testament / rome / apostles in general, also had the desire to save Mikuru / Jesus (take Pontius Pilate trying to save Jesus from the Jews for example), but can't because of Haruhiism / Judaism / OT God's will.
 * Also, we (and otakuism in general) feel better when Haruhi abuses Mikuru. This means, Mikuru didn't just suffer for Haruhi and Kyon's sins, she suffers for the sins of the otaku community in general.
 * Which means she is also Kamina's relative, with Haruhi Suzumiya being the distant past of TTGL....
 * Where does Yuki and Itsuki fit in?
 * The angels! More specifically, Itsuki is the equivalent of Gabriel (Messenger) and Yuki (or IDE to be exact) is the equivalent of Michael (serving as the "army" of Haruhi, after all she leads the SOS Brigade to success after success).
 * So  is Uriel? Where does Tsuruya fit into all this? She can't be Joseph Smith, and I don't yet know enough about LOLFANG-tan's business with the SOS Brigade to pinpoint her place in this.
 * No need to specify, Yuki and Itsuki are the angels who preached the coming of the Trinity of Haruhi, Mikuru and Kyon. Nagaru Tanigawa in turn wrote the Bible.

Mikuru actually comes from a quite recent future.
Haruhi's powers will cause a kind of Technological Singularity only one generation in the future, which will turn the old technologies utterly obsolete in a matter of few years. Mikuru is in fact first generation to have never have had any contact with the "old" technology, and the sheer amount of new development has caused the mainstream culture to largely lose interest in the recent past, save for the vital time travel services to keep history under control, which is why she is so helpless with contemporary tech despite of essentially being a time agent intern.

Asahina Mikuru is more capable than she appears.
As far as her own time period is concerned. That she understands the mechanics of time travel enough to realize that Haruhi is the origin of the theory shows that she's not completely stupid. She's also able to completely grasp Nagato Yuki's technobabble with little effort, so long as it has something to do with spatial manipulation. Furthermore, we've never been shown anything in regards to her grades in school, so it's possible that she's much smarter than she appears. It's just that the vast majority of her knowledge is pretty much completely useless in the "present" time period (such as her lack of familiarity with modern technology), so she's effectively still more or less helpless either way. If there ever comes a time in which Asahina Mikuru is allowed to function in her native environment (i.e., the future from which she came), she may gain an astonishing level of competence for that duration.

Mikuru has a way of subconsciously influencing tropers.
I have seen at least three separate occurences of a recognizable section of her name being inserted into long words in Suzumiya Haruhi no Yuutsu-related subjects three separate times. Two is a coincidence, three is a pattern.
 * I thought three was enemy action.

Mikuru asked Kyon not to watch her the first time Haruhi started stripping her because she knew Kyon was unlikely to physically intervene.
Mikuru was given a briefing on Kyon's psychological profile before embarking on her mission, and she knew that Kyon had an extreme reluctance, at first, to actively forcing Haruhi to not do what she wished. Therefore, Mikuru believed that Kyon would try to talk Haruhi out of stripping her without actually restraining the girl, which would leave Kyon doing nothing to help Mikuru as she's being stripped right in front of him. Rather than suffer that embarrassment, Mikuru asked Kyon to leave rather than make an empty gesture. (Okay, said like that, it looks like option b, Mikuru is a spazz, is more likely. Or the even the somewhat unlikely option c, Mikuru is secretly letting herself be abused because she knowingly and deliberately accepted a mission to go back in time and become Haruhi's pet in the hope that she would gain some influence on the reality warper.)
 * Wasn't his making a move towards them the thing that caused her to scream? In other words, wasn't Kyon already doing more than just telling Haruhi to stop?

Mikuru is from 200,005,600 years in the future.
Haruhi says to Kyon in Disappearance: "Come back in 200,005,600 years if you want to sneak a peek at Mikuru's underwear!" Things Haruhi say tend to turn out to be randomly true, and remember that Mikuru's not allowed to be in a relationship with people not from her time period, so presumably Haruhi is saying that if Kyon were to exist that many years into the future then he would be allowed to be in a relationship with her. It's likely that she's not from the near future, because apparently in her time period, boats don't use buoyancy to float, and that's not going to change for quite a while, so the number Haruhi gives is plausible. However, that brings up questions like "Has evolution stopped well enough that humans remain the same, even two million years into the future?" "Did human evolution stop when Haruhi eventually dies?" "What happens to Haruhi in the future?.

Mikuru is Kyon and Mikuru's daughter via Time Travel.
Mikuru is Kyon's daughter and granddaughter and great-granddaughter...

Mikuru was born into poverty.
This is why she's so useless with current technology and history: her access to education was severely limited. Surely in the future there might be something in place to give all people basic educations, which is how she knows of a few things, but not a whole lot. The reason Mikuru interns at the Time Travel Agency is to try to earn enough money to escape, and get a chance to go to school (archaic as the lessons may be) in the process.

Time travelers are rare because?
Why are time travelers so fnording rare? We've seen four interfaces and at least half a dozen espers. The interfaces and espers both claim that there more of them running around out there. But so far we've got exactly two time travelers and the shortage is so acute that Mikuru has to touch herself to get things done. So why is this? Note to the future: If your present reality does NOT include billions of human beings, please time travel to change your timeline rather than reinforce it.
 * Only immediate descendants of Haruhi can stand up to the Butterfly of Doom without getting blow away by their own paradoxes. Therefore only Haruhi's daughter and son can time travel without going poof.
 * In the future everybody is constantly plugged into the Matrix/World Wide Web/Mass Mind, etc. Disconnecting citizens from their endless supply of kitten videos would kill them from the shock so you have to raise time travelers in a disconnected mode, even if this makes them idiots.
 * Only a very few people have the gene that allows them to travel through time. Note that Kyon and Mikuru share at least this one gene...
 * Time travelers are rare because time travel is neither a medium nor well done.

A future Haruhi is Mikuru's superior.
Mikuru has already said that Haruhi will have founded her organization so what if Haruhi is still around giving orders to adult Mikuru to give orders to teenage Mikuru?

The time stasis from Tanabata was to freeze in the timeline.
In order to make a change in the past stick, the time travelers have to live out the period after the change. Otherwise it either gets undone or drifts off to a slider dimension.

Mikuru was chosen to seduce Kyon.
They searched the entire population of Earth to find the right person and they trained her against their historical models.

Mikuru is a slider
The Melancholy of Mikuru Asahina reveals that there are multiple futures. She came from one possible future into present time to ensure that her future will occur. Therefore its possible that the present she is in now is headed on a different path, and she slid into the dimension to change that.