These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
YMMV: Rune Factory
Base Breaker: Some fans think Mist's cute. Others think she's annoying. The fact that she's supposed to be part of the Official Couple hasn't helped at all...
Ensemble Darkhorse: In an official Rune Factory 2 character popularity poll, Barrett ranked in first place, beating out Kyle (the main protagonist) by about 100 points.
From Rune Factory 3, Sofia, Pia, and Raven are the top 3 bachelorettes in terms of popularity.
Yue got a LOT more popularity than was expected. So much so that she makes a cameo in the third game selling her wares again.
Fridge Horror: If Herman is his father... what's Max going to grow up to look like?
Made worse by the de Sainte-Coquille character from RF4 who looks just as swollen as the rest of the adult family, but was apparently a looker in his youth. If you try and imagine him younger and thinner, you get something similar to Max.
Fridge Logic: In the first game, you need permits to enter any dungeon. However, how do the NPC's manage to enter the caves without needing them?
Perhaps they have permits already?
Game Breaker: Arguably, the wireless dungeon under your house in Rune Factory 3. Accessible early in the game, it provides the player with an absurd supply of income, items and equipment (especially on the higher levels), all with no penalty for fainting if you choose the multiplayer option.
The games are chock full of this. For RF 1, some of the female friendships seem romantic in nature, and in RF 2 there is a romantic sounding dialogue Max gives Kyle, comparing their relationship to a fine wine. Those are the most YMMV options. In RF 3, if you give Carlos his favorite dish, his dialogue, after a pause, ends with a blush and a "...Can I kiss you, bro?". (Micah responds with "N-No thanks!") If you marry Lara in Frontier, Selphy says "I know she'll be the best wife because I actually really want to marry her!" Furthermore in Frontier, if you take the flower bouquet and propose to anyone (including the guys), they all will get a blush and heart effect on them. (Not to mention some of their starting lines sure sound like they might accept.)
Les Yay: In Rune Factory 2, you can court and "marry" a pair of twins, regardless of your gender. Together. However, in the English version, they act oblivious to marriage and talk about toast the whole time.
However, it is kinda cute in context.
Launcher of a Thousand Ships - A rare in-game example, in Rune Factory 2, Yue the wandering salesgirl. Most of the marriage candidates, if you don't get married to them, will eventually wind up married to one of the other NPCs. If you marry one of those girls, Yue winds up married to whoever that girl would have eventually married in the first place; presumably this is to ensure that everyone who is supposed to be married as of the timeskip actually is, since many of the new post-timeskip NPCs are actually the children of the townsfolk from the start of the game.
Narm: In Frontier, activate the events involving the Big Bad, Gelwein, on the Pumpkin Festival. Now try to take the events seriously as he confronts you with a Halloween pumpkin mask on his head.
Alternatively, in Rune Factory 3if you marry Raven, it is possible to trigger her birth cutscene when she is in phoenix form. Impossible not to laugh as she groans and Micah rushes her to the clinic.
The first game's ending involves a dragon that breathes plant life coming to save you all from the Sechs Empire's tanks in the nick of time. It's as silly as it sounds, and the fact that the game script shortly thereafter blatantly misspells "swordsman" as "sowrdsman" does little to help matters.
Replacement Scrappy: Jake who replaced Nicholas from Rune Factory 1 as the love interest of Cecilia.
Especially in Oceans, considering that Aden gets over twice as many potential brides as Sonja. Not even justified, as several female characters could have been male without changing the story. Elektra, Sierra, and Pandora come to mind, not even bringing Mikoto into the mix.
There actually is a justification for it. Sonja being a playable character post plot was a decision made relatively late in the development of the game. Mikoto still probably could have been swapped out for a boy who's mistake for a girl rather easily.
This is changed in Rune Factory 4 as the male and female main characters both have the same amount of bachelors/bachelorettes.
What Could Have Been: The first Rune Factory contained unused sprites and character models in it, including one that looks like Brodik from Rune Factory Frontier and the guys from Kardia in wedding attire. They were possibly going to be love rivals for Mist (Zavier), Rosetta (Lukas), Melody (Camus), and Tori (Russell).