The lack of S Links with your Party Members (and the ones that are there are locked behind stats).
I am really enjoying the game, it really is, unfortunately, a lesser P4 but it still has its own charm and quirks that are great, hitting on girls at the beach was pretty great. But the lack of S Links with ALL of your party members is just depressing. In P4, even though I didn't use him or her at least I got to have a connection with them, got to know them, advance their character arc (and a nice bonus in creating personas). In P3 I have my set team ( Yukari, Akihiko, Mitsuru) and since the other members don't scale they eventually become worthless in battle and since there is no S Link, they really are just cannon fodder for me. (Any tips on keeping a team balanced would be welcomed cause I do kinda hate being locked into the same 4 everytime)
Sure there are other nit picky things that bug me here or there but they don't bother me near as much as this one. I am enjoying it as I make my way slowly through it, story is ok, kinda have some ideas what might happen with characters but it is just a hunch at the moment (currently in mid-September). Really playing this game is getting me psyched up for P4G, any excuse to play P4 is good enough for me.