Both are great, so I don't think it really matters. We've stayed at four different sections of the resort over the years (once at Fountains I). I liked them all (no complaints whatsoever). Gina, a frequent poster, on this board, owns at Fountains and reported that some of the buildings in that section have gone thru a remodel too that is really great (so some units there are probably the most up to date in the entire resort). Fountains is her favorite section, and it's lovely. In general, though, the entire resort does a pretty good job of keeping things nice.
I was debating the same thing (Fountains or general section trade) and ended up doing a trade to the general section, but mostly I think because I have my dad with limited mobility with me and thought in the larger Village area there would be more options with ground floor and some sections with elevators too that could accommodate him. I'm sure that would have worked for Fountains too. In my thoughts too in my picking general is I will have some 20 somethings with me who I could see walking to different sections to check out the entire resort, and I think that might be easier in the main area. We also like to play tennis at the clay tennis courts at the Courts and will do that multiple times during the week, so it might be nice for us to get one of the sections right next to the courts. (We are a big tennis playing family FYI.). But except for accommodating my dad, really and truly these others things are nice, but are no big deal.
I think you can flip a coin. There is not a bad choice. This is a great resort IMHO.