Story of Seasons/WMG

Your character is a descendant of the Harvest Goddess
Why else would she do you so many favors and grant you so many boons? She looks after her own. Of course, this puts the games where you can marry her in a whole new light...

The main Character is Actually an All Powerful Dictator/Messiah/Time Lord/God/Haruhi/Ect...
{S)He communicates with spirits, collects mystical objects, regularly talks to and orders a goddess to do his/her bidding, and has brain washed everyone with "gifts" into doing what ever (s)he wants.
 * Well, damn.

People in the land are sterile.
Think about it. In whichever town/village/valley/whatever you choose to play in, it's rare if any of your rivals and their spouses to actually have kids. Take Mineral Town for instance: Cliff and Ann are married for 80 years and have no kids.Sure, maybe they don't want to have more kids, but all five couples? A little unlikely. The reason why your character can have kids is because you're new to the land, so whatever makes the other people sterile (the water, radiation...) hasn't effected you yet. It will eventually, that's why you usually only have one kid.

Whatever it is that affects them, it only affects your gender; that's why you can have kids with someone from the land.
 * Note that this is not the case in HM64, IoH and Animal Parade.

There is no rule against clergy of the church of the Harvest Goddess marrying, you just can't marry the priests in Harvest Moon games mostly because there would be nobody to preform the service.
And eventually, once enough games are concurrent with other games, the remakes will allow you to call a priest from another town to preside over Carter's any town's local priest's wedding. There have been plenty of secret bachelors and bachelorettes, without rivals, so all they would have to do is add a few extra events to the game, and maybe a prerequisite or two.

The people of [insert location where game takes place here] are cursed to be forever young.
The Harvest Goddess must have done something to make them effectively ageless/immortal, or at least age VERY slowly (Like when Ellen dies: she was probably slowly and painfully dying for thousands of years and couldn't do anything about it.). It's a horrible life because you never mature and would probably run out of things to do. That's why a lot of people seem to wander aimlessly by the time you show up: their lives have become empty until another person showed up.

Their world has an Alternate History from ours
Obviously they must have in one way or another been affected by their magical beings other then religion wise. Also, their world seems quite a mash of Europe and Japan. The main religion from where the games are set are a mash of Shintoism and Catholicism. Quite a few characters are European or at least not Japanese (as shown by their names in Japan, and their designs) and quite a few are Asian (mostly in the Wii games). A lot of the games are distinctly European, yet Japanese food and festivals are still ever to present. Something in their world caused Japan and Europe to become comfortable with each other, or possibly they're even one nation

3DS will be a remake of 64
It has been 12 years, and the 3DS has quite a few remakes of its sleep as of pre-release.
 * It will also have Sara as the female protagonist.

Pete had two children in canon
One was the 64 protagonists father or mother and another was one of the bachelorettes parents.

Ellen in 64 is really Ellen 2
Aka she's not the Ellen from the original games, but her daughter who they named after their mother. What she said her job was is different from Ellen in SNES. That would also bring the potential Brother Sister Incest / Kissing Cousins Unfortunate Implications of 64 into distant relatives, similar to the potential in DS and Cute.
 * Possibly Jossed, since apparently you and Elli are the Official Couple.

Shortly after the end of the game, a horrible disaster strikes Forget-me-Not Valley.
Right after  at the end of the game, an earthquake suddenly hits the valley. Tons of debris come off the mountain, and Rocks Fall Everyone Dies. However, shortly afterwards, all of the townspeople reconvene in Fluffy Cloud Heaven. Since, for them, heaven is home and family, all they truly need to do is rebuild their valley to be happy again. So the townies use their mental power to construct a perfect replica of Forget-me-Not Valley in Heaven so they can live in peace and happiness for all eternity.

This is why

The citizens of Forget-me-Not Valley are cursed
Same as an earlier theory, but with a different explaination. Throughout the game almost everyone stays about the same as they were when you first got there. What makes this theory more believable is which people AREN'T affected; Hugh, Kate, Lumina, your son, and you. The curse seems to only affect adults, so Lumina, Kate, Hugh, and your kid are safe. There's another theory higher up explaining why you're not affected. Carter and Flora's excavation site is actually them looking for a way to break the curse, which is on those tablets you find.

The games take place in the 50s - 70s
It has a vague time period feel, but in all essence it feels similar to that time period. The DS games take place one hundred years in the future but that would be a "Twenty Minutes Into the Future" type case. The FOMT and MFOMT games take place at the same time and seem more modern though, so FMNV may just have a retro feel since it's in a valley and rural. Maybe it's in the 80s. But 70s seems like the best bet for both series together.
 * Maybe even the 20s since the world seems rather advanced thus it would be Schizo Tech.

You die for some strange reason
It's obviously odd. You're in your early twenties when you first become a farmer, and twenty years later you die. Even the senior citizens are still kicking, and they must be in their 90s. It's possibly you died due to overworking, stress on the body, a farm related disease, not taking care of yourself, etc.

Takakura is an immortal who feeds on souls.
Think about it. Your character's father suddenly dies and Taka calls you out of the blue to ask you to run the farm. And then once you've aged sufficiently, he eats your soul, causing you to suddenly 'pass away.' He's clearly a lot older than you and even outlives you. Bonus fridge horror when you consider the possibility that he consumed Nina's soul too, and is plotting to target your character's son next.

AWL takes place in the 70s
The fashion, technology, etc all fits.

You and Jamie are the Official Couple
All the other bachelor/etttes have love interests. Jamie takes quite the interest into you, and you to him. The game also ends if you marry him.

The games takes place in the AWL-FOMT universe, which in itself is an AU to the 64 universe
Nami appears, presumably before she goes to FMNV (or possibly in canon Mark marries Celia and Nami goes away). This would explain why the characters are alive and concurrent with characters born way after them. The STH gang moved away from their town for some reason. Alternatively..

A lot of characters are reincarnations of the SNES, and STH, gang
Take DS to AWL-FOMT. It takes place one hundred years after and everyone has an Identical Grandson. Nami doesn't appear to have been in Forget-Me-Not, the STH gang don't appear to have ever been in the their STH town (or have met Tony), and the SNES gang are alive and modern. This would make this game set in the 64 timeline, which is also set in the To T timeline.

If there is a sequel-type remake of Magical Melody, Jamie will still be the Official Love Interest in the form of a Third Option Adaptation.
Jamie will reference having been in love, once, but that person is No Longer With Us, and Jamie never gives enough details to determine which (if either) of the MM protagonists was the former love interest or even formed a relationship with Jamie. If you marry Jamie and express a wish to have a child, the mayor (or somebody) will show up with a Door Stop Baby (a la DS Cute) regardless whether you're male or female.

The special girls are in love with you but are afraid to marry you
This applies to only the En. versions of Cute. Look at their reactions, specifically Keria (she gives her uncomfortable look with a bunch of eclipses before "She looks troubled"). They are in love with you but they feel frightened to marry you being that you're both female. You do live in a small country town, though everyone seems open minded. Not that they know though. Plus there's the whole both being female" thing. In the JPN version this is why they go under "best friends" instead of "wife"..Also because the latter is probably illegal.

The Witch Princess wasn't breaking the fourth wall in DS
She thinks this is all a 'game' to her. She's a mischievous, playful witch so it wouldn't be too far fetched.

These games are AU from AWL or non canon
There's a lot of faults in the timeline between the FOMT, AWL, and DS.

Charlie is part Harvest Sprite.
How else do you explain how a kid who can't be older than Eight can create talismans than can double your stamina, regenerate it, make people like you better, give you super speed and even slow down and speed up time?

Karen and Popuri are "more than in-laws".
Popuri's glad Rick didn't come with them because he'd keep her from spending quality time with his wife.
 * Alternatively..

The main character can read minds.
Think about it. Maybe they can't read "minds," but they can read their hearts. That's why you have that page, the one that lists how close you are with people. Perhaps the player had a near-death experience when their ship was struck by lightning, and now they have this power.

The male lead dyes his hair.
Think abou it: How could your/his wife have a brown-haired kid if they're both blonds or some other recessive gene? (Other than the idea of an affair, but this is Harvest Moon, people. Obviously, the boy has brown hair and just dyes it for some reason. (maybe to look different from other protagonists?)

As to how to manages to get this dye, Chen did it?

Taro is an older version of Pete.
Seriously, just look at him.
 * The manual and official sources stop just short of stating this outright.

Julius has Single Target Sexuality
He's every bit as camp as he looks, but like most people, he's got some "flexibility" (paging Kinsey). If it's Hello Insert Name Here or Candace, it's OK.

Alternatively...

Julius is actually straight as an arrow, but feels more free to express himself in a small community.
The Harvest Moon towns are generally pretty friendly, accepting places, and everybody knows everyone else pretty well. They're more like really big extended families, and thus they learn to deal with everyone else's weirdness. When Julius was growing up, he discovered he liked fashion and gems and other "girly" things. Because there probably weren't too many other kids around, he didn't get teased, and, in adolescence, there wasn't as much xenophobia (in the literal sense of fear of the different), so he didn't feel the need to hide his true self out of the assumptions others might make. And, as he grew up, everyone got to know him and who he was and was perfectly OK with him.

Sure, Real Life small towns can be close-minded too, but the HM games are such a Sugar Bowl it's hard to believe that of one of them.

Julius used to be a member of a Visual Kei band.
It would certainly explain his FABULOUSNESS.
 * That... actually makes so much sense, it's scary. Though it doesn't explain why he went from music/fashion to... metalworking.
 * After a couple years of performing, he realized he was more interested in the fashion and jewelry aspect than the music, with particular emphasis on the jewelry, so he decided to focus on that. There you go.

Toby is Gin Ichimaru from Bleach.
He manages to survive the whole series and eventually retires to a nice life spent fishing.

Mira's husband is/was a mayor.
In the town's graveyard, there are many graves, but you can only read three. One is for Tom, who came back as a ghost to search for his lost love Anna; Mary; and the "Graves of mayors past". Since we can confirm Mira had a husband, not a wife, her husband's grave would have to be scattered about in the many mayor's.

Jin was going to be female, but still the other half of Anissa's Rival/Love Interest pairing.
Someone on the Headscratchers page mentioned that Jin looks like a girl. It is true that his concept art is extremely androgynous, and seems plainly feminine if you misread the chain holding the sides of his lab coat in as an underbust shadow. Jin is also a Gender Blender Name. According to the Harvest Moon wiki, Anissa will follow the romance events with a female protagonist, only stopping after "infatuation" but immediately before the option of marriage. Ergo, Jin was almost a lesbian. Their son was artificially conceived or used a sperm donor or something, if he wasn't adopted (possibly from a geographically distant family member, in the case of adoption). Both have been used before, the latter with Best Friend Ceremony adoptions and the former with livestock fertility potions.

Jin is Jin.
Names the Same, and don't tell me you don't ee the resemblance. It's utterly uncanny. Alternatively, Jin is Jin's ancestor.

Zephyr Town turns it's inhabitants into brain-addled drones
Zephyr Town is a malevolent Genius Loci. Think about how your character reacts with a "Yay!" when s/he falls through the ice in Winter. How when s/he climbs out of the river, he reacts with the same glee if s/he finds a gold nugget or a stick. The way your spouse will stop talking about your child about an hour after s/he's born. The way every festival will draw the same lines from the townsfolk. Zephyr Town itself molds them into their separate Stepford-like roles, only making exceptions for whomever you marry (switching their role over to "your spouse") And once they settle in, they can never leave for long. Anyone who manages to truly break free (Like Stuart and Ethel's son) take care never to return, lest they be re-ensnared.