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.
Don't forget about Melody. She's so well liked that they made another character that looks similar in Rune Factory 3 and clearly expected her to be one of the most popular, as evidenced by her presence in the first OP.
Fridge Logic: The recipe given for the wedding bouquet is said to be part of the tradition for proposing to someone in Trampoli, yet it requires an ingredient that can only be found on Whale Island, which was inaccessible until Raguna grew a path to it, so how could there be any married couples in town without a needed ingredient for the traditional bouquet?
People get married elsewhere and move here.
The real question is why they even pretend it's a tradition. Eunice's parents are the only married couple in Trampoli, and they tied the knot before showing up. Since the town was founded by Stella, who is herself single, anyone before Raguna who got married in Trampoli would've have to have moved out.
Normally, it doesn't make any sense to be able to create an entire jar of jam using a single strawberry, but did you see how huge the fruit are in this game?
Game Breaker: The Runey System, either in a good way or a bad way. Bottomlined, having a lot of prosperity areas can make crop growth ridiculously fastnote At 6, onions grow at the same rate as turnips., but if you don't take care of the Runey balance quite often, you'll be waiting for weeks for a turnip to grow.
That's just a con for not taking care of Runey population properly. And properly taking care of it is another story...
Scrappy Mechanic: If you don't like it, the Runey System. Basically, you have to balance out nature spirits (Complete with their own food chain, so they never STAY balanced) by sucking them up with an inefficient "Harvester" and spreading them out evenly throughout the world. If you do it right, your crops will grow much faster (To the point of Game Breaker status; see above). But if you ignore this (Or aren't aware of the need to do so) the runeys will die out. And Runeys dying out in even ONE AREA (There are 7 or 8 areas) of the world can cause crops to take much longer to grow (Up to 4 times as long!) and/or randomly die in your fields. Needless to say, it has caused a case of Broken Base.
While those that like it point out that it can speed up crop growth and can be streamlined, critics have some valid points when they point out that it's fairily inefficient, tedious, and NOT optional at all. Simply put, if you don't spend a good chunk of time on the system, you can kiss your chances of farming goodbye as your crops take forever to grow and randomly die.
To clarify on why it can be love or hate, you need to collect different Runeys and release them in order to balance them out (on top of natural death/growth rates). To collect them requires using an item to suck in near by Runeys. However, doing so results in a good 4 second or so animation and it only sucks up Runeys very near you (around 12 or so in a crowd) and it does so indiscriminately (you can't pick which ones you want and you will suck up everything in range). You can't move while this is happening either. Releasing them also results in a long animation (and you can't move). And you need to do this for many areas each of which can have tens of different Runeys spread all over the area. The result is that while the mechanic isn't necessarily bad, the means to interact with it is long and imprecise. If you want to suck up only 2 near by Runeys of a specific type, you end up having to suck up all nearby Runeys and then release the all of the Runeys except for the 2 you want.
The worst part is that the game and the manual don't really explain this at all. They mention it, but don't explain any of the finer points. To truly understand how to make it work you'll have to look on the internet.
That One Boss: If you don't know the tricks, all the bosses will qualify, even if not at first. But the dungeon bosses just outshine the storyline bosses in particular; in addition to their massively towering sizes, they can ass-whoop you in a few hits even around the first time you fight them. On successive visits, they'll be waiting for you with a new bucket of kick-assery. Even that fades in comparison to their post-endgame power-ups, where their stats are buffed up 2~3 times to hit three digits their original, with their HP literally Over Nine Thousand hitting FIVE digits. Have fun dying!
However, two dungeon bosses need to be defeated only once, and the other two are just optional. But chances are, you're gonna need to fight them sooner or later, since you need their unique drops for... your kid's toys.