Story: simple seems best for me. "You had an uncle/aunt/distant relative, they have passed on, and their will stipulated the farmland be passed on to their favorite grandson/niece/nephew/whatever". From there, it's all really about developing the friendships/romance, and doing the farmy-thing.
QUESTION: Do we want a singular entity, like a Harvest Goddess, or do we want things like Faeries? Or both? Because I actually have this great idea about applying some of my Celtic Folklore to the game, in the form of household and domestic spirits that could be employed to help you out with things. If this seems like a viable idea, let me know, and I will expand upon it with details; if it's a no go, don't worry about it. I've got my big boy boxers on.
QUESTION: I have not played any of the Rune Factory games, so I would need someone to point me in the direction of a good wiki article, or give me a synopsis about what these boss dudes are.
Idea: Power berry system seems like a good idea. I would also like to see something done with cooking, as I mentioned before; eating well gives you stamina bonuses, but never penalties for not eating right. This could be an optional thing, of course, something to think about once we've actually got the core stuff done.
Idea: People should occasionally comment on the state of your farm. Obviously it's run down at first, and folks will know that you've got a lot of work to do, but, say, after the first year, they might start saying things based on how upgraded it is?
For instance, if you haven't upgraded anything, the carpenter might say "You know, I could make that place a whole lot better for you", or other farmers may say something like "Don't you have any self-respect?" Or perhaps something not quite so mean, if we want it to be happy-go-lucky all the time.
Idea: I don't know about a gang. If we went full fantasy, it could be something like evil goblin raiders! But other then that, I don't really see a gang being interested in some Podunk place like Agriculture Town.
Idea: Butcher can be done, but if we cut out the hunting part, that might... well, actually, we will still have the cow/chicken/other animal raising, right? Definitely can work with that.
Idea: I like your idea, Swissfag, on the VN like dating aspect. Furthermore, I have an idea about the friendzoning thing, where, after you get the friendship bar high enough, you get a dialogue choice, akin to:
"You feel like you could take this relationship to the next level. Do you ask [character] on a date?
>Yes
>No"
Choosing no keeps them as a friend (with maybe the chance to date them in the future?), choosing yes will lead to the dating.
Idea: Another optional thing, for if/when you get a wife. Marriage feast! If you're good friends with different people, you'll get a slightly different occasion; for instance, if you're Close Friends with the bartender, he's brought out the champagne for this event. You and the baker are bros, and there's a god-tier cake for everyone. Etc.
I will see if I can find anyone else to help. I do have one friend, who may contribute more thoughts/writing, but I don't know if he can code.