Devil Survivor has some great story too it. It's a megami tensei game (ie, by the guys who made persona) but the graphics and gameplay are pretty subpar. So this is NOT what you are looking for.
Other than that... I'm kinda out of the gameloop. I really enjoyed skyrim, though all the other games on both your lists (except KH2) are games I pretty much dismissed out of hand games I knew I wouldn't like.
Seriously, Golden Sun and The Lost Age for GBA. Do it if you still have a system that can play it. Other than that... I really can't say there were many games with great story and gameplay.
Well, get custom robos for gamecube and gamecube controller to play on your wii. story is ok, but the gameplay is where it gets fun.
Halo and CoD online multiplayer is where the fun is at, but not what you want if you're really looking for campaiging, even if halo coop campaign can be fun.
Dark souls... well, it's way too easy to come to dead ends and impasses. you could play 10-30 hours and not get anywhere.