Dragon Quest V/WMG

The hero is an Expy of Krillin (or at least based on him).
He just as much of a Woobie as Krillin, his 'canon' wife looks almost like Android 18, Krillin's wife (and if she was a Tsundre she would fit 18's characterization like a glove), and the hero's relationship with his closest friend started off pretty rocky, much like with Goku and Krillin.
 * Except that Goku was never a spoiled brat. A violent baby monster maybe, but never a spoiled brat.

The twins are not children of the main character
The day/night cycle is pretty damn explicit. The time between "hero reunites with wife-to-be, gets married" and "children born" is a couple of weeks, two months on the absolute outside for the grinders. The only reasonable conclusion is that whichever wife Hero chooses, she's already at least seven months pregnant (presumably by a Zenithean).
 * How about...gaining experience points and levels speeds up pregnancy.
 * Plot Relevant Age Up? Or the cycle is simplified -- really, sailing across the ocean only takes, what, one to two in-game days at most?
 * You're assuming that the humans in this game have a nine month gestation period.
 * The day/night game mechanic doesn't represent in-game time as wholly as you seem to think. One day that the player goes through is certainly not the equivalent of one day in game-time. The time between the hero and Harry leaving Maria behind in the Abbey and their return is implied to be quite some time; this troper would predict at least a month had past. But if you go by the game mechanic, as few as two days have passed (one day spent at Fortuna to get the wagon, one day travelling to Coburg and teleporting back to the Abbey). It's made explicit that more time passes in game than the player thinks when you finally rescue your wife. If you party-chat with your kids, one of them will mention that it's taken them two years from rescuing you to rescuing your wife. In that time, you the gamer do about five or so plot-relevant quests. So from that information, it's not too large a leap of logic to assume that it takes you and your wife nine months to travel from one end of the continent to the other, especially considering that a) it's their honey moon, so they'll be taking their time and b) you stop by every interesting spot along the way looking for the Zenithian equipment.
 * And the day after the twins are born the game actually makes it clear that four years have passed since the second section of the game began; he was six in the first section of the game, ten years passed during the timeskip taking him to sixteen, and then that night when he talks to the nurse holding the twins she tells him that the night his mother gave birth to him was twenty years before. I'm guessing that he only got married about three-fourths of the way through that, but that would still give them a full year for his wife to conceive in and the twins to be born.

Debora's Rich Bitch nature is directly connected to having Spoiled Sweet Nera as her "perfect" sister.
Nera has elements of a Purity Sue to her: practically everyone who knows about Nera talks about how sweet, wonderful and perfect she is, holding her in sharp contrast to her older sister. While Debora certainly isn't The Unfavorite, as her parents still care deeply for her and spoil her rotten, there are hints of them wishing she was more like Nera. No doubt Debora is keenly aware of this. Note how she claims that Nera's suitors are actually interested in her; this could be denial, or pretending that she isn't aware that everyone prefers Nera. She's definitely spoiled, but to a certain degree beyond that her nasty behavior is an act, pretending she isn't hurt by the knowledge she's not nearly as beloved as her dear, sweet sister. To acknowledge it or attempt to change would be admitting defeat and conceding that her sister is superior, something Debora's far too prideful to ever stoop to.

Debora had quite a few reasons to propose to the hero:

 * 1. She thinks he's a Gold Digger, and giving herself as a third option is her way of protecting her sister. (She was probably right initially, the hero came to the town for the Zenithean Shield and didn't need much prompting to enter the competition for Nera)
 * 2. She's impressed by his occupation as a Monster Tamer. (She does seem the type...)
 * 3. She knows that no one else would take her.

Flora and Nera are different people.
The difference? Flora was an only child; Nera has an older sister. Alternately...

Debora existed in the original games, but...
Debora was born in all of the games, but died due to Diabolus Ex Machina before Briscoletti could do anything to help her. When Diabolus Ex Machina was dialed back in the remakes so that Bianca could live happily without marrying the hero, it weakened it enough that Debora got to live.

Future remakes will add another candidate for the Heavenly Bride.
Because Debora set a precedent. Adding more brides will be an easy way to convince players to buy the games again, and will cater to other interests -- just as Debora is meant to catch the eyes of Tsundere lovers, the new girls will be designed according to whatever's popular at the time. Possibilities include: All of these new candidates would stick with the hero until the Engagement Challenge, then leave if not chosen, allowing them to function as Guest Star Party Members and potential Crutch Characters until he can build up a good stable of monsters.
 * Prince Harry's heretofore-nonexistent sibling, to bring in the green hair. Suffers the same stint of Break the Haughty as her brother, and also runs into the whole Heir Club for Men issue.
 * Even if she is out of the running for the succession, it's highly doubtful that either the Real Queen Mother or the fake one will let her live if she stays in the castle, which means that we can probably add (through euphamistic means) the Soiled Dove issue too.
 * A hired blade who the hero can pick up for protection soon after starting the second phase of his journey. A Hot Amazon Ladette with no magical ability. Develops a Bodyguard Crush on him over the time they spend together.
 * A Cowgirl from Hay who's impressed by his monster-training abilities. After he's falsely accused of running a Monster Protection Racket, she attempts to defend him, then offers to join him by way of apologizing -- and also to try and learn how to train monsters herself.
 * Honey/Bella (if you decide to expose the Fake Queen Mother before picking up the Cherry Branch).
 * Maria/Marina (If you go on the ring quest first)

Future remakes will make it so that Bianca arguably ends up happier if she doesn't marry the hero.
The original had her hit by Diabolus Ex Machina if you didn't choose her. This was toned down in the remakes, particularly the DS version, so that players wouldn't feel as guilty marrying Flora/Nera or Debora instead. Following this trend, future remakes will put forward the possibility that she arguably ends up better off if she doesn't marry the hero. Nera already demonstrates the logic behind this -- if she doesn't marry the hero, she still winds up Happily Married and is spared all of the trauma, tragedy and trials that the hero and his bride/family face. Bianca will get a similar happy ending if not chosen, finding someone just as suitable and having a good, peaceful life without all that drama.

Your hero kills the Evil Chancellor.
He personally betrays you and Gotha out of his own short-sighted Greed and has your wife kidnapped. Though Rewarded As a Traitor Deserves, he survives his injuries long enough for you and your monsters to come across him. The last words out of his mouth are him begging for your forgiveness, and he is cut short. Alternative Character Interpretation and This Is Unforgivable! takes care of the rest.

Bianca is biologically Nera and Deborah's half-sister
Whitey has a bit of dialogue shortly before the marriage segment where he confesses that Bianca isn't really his biological daughter. By extension of logic, all three women have Zenithian blood, since whoever you choose bears the Chosen One. Furthermore, Rodrigo's lineage is explicitly stated to be special, considering the whole deal with Bjorn, so it's probably safe to assume that he's where the Zenithian heritage comes from. However, she can't be his wife's daughter because of her blonde hair color. My guess is that he had a fling with Bianca's mother some nine years before the story began and was told sometime later that she was with child. She would have left Mostroferrato to protect Rodrigo's reputation. After you bring her back for Rodrigo to meet, it's possible that he realizes who she is and that's why he's willing to give you the Zenithian Shield and finance your wedding even though you don't marry Nera as per the original agreement.
 * One problem with this theory: If you marry Nera or Debora, you find out.
 * Alright, amendment. sisters. Ruins all the fun of, though.