man there are a lot of things jrpgs do wrong... a few to name a few:
can't save when ever and were you want
BS like bosses being immune to every spell and status effect ever made. seriosly, I had to fight some Shiva clone boss thiing in FF12 and no magic worked on it. not even fire. the only thing you could do is equip ice sheilds that half the damage to ice, have your tank character plow into her and keep your others as far away as fucking possible casting heal and haste and shell.
somtimes enemies get to attack twice in 1 turn if it's turnbased or little freebie attacks like in FF12 that are fuckin like the plague that give you every single status effect known to man kind ever to all your party members.
man sometimes the hardest enemies ever revive them selves to full strength by casting some magical spell you can't learn. this happened in FF12 a few times too, some bosses would just cure itself full of Hp while your sitting there running out of potions and shit and your Mp is all gone.
sometimes the movement speed fustrates me, even when you have a run button. actually this one applies to many games, like Mass Effect(only run in battles), Morrorwind(walking is reallly slow AND running is like 2% better), Halo(mister chef can't run?), ff12(every monster moves faster than you) and etc... though the problem isn't always the speed, it's the distances between plot points usually due to bad design. especially when you have to backtrack because you forgot something or the game is being stupid and isn't clear on what to do so you go back a long ways and find out you have to go back again.
maybe this is because I'm a good runner irl but seriously it seems like some characters just move so sloww...
also ff12 had so much crap to put up with looking back...