Sora wanted to stop Organization XIII because he disapproved of their methods. While they only wanted their hearts back, they were pretty nasty in their methods of achieving that goal. Whether or not their goals can be justified doesn't change the fact that their methods cannot.

I've no idea about changing to Wisdom form right before the 1,000 heartless battle. As I've never heard of that working before (but heard plenty of complaints about not being able to do it, I imagine the answer is no.

The Disney worlds in Kingdom Hearts are rarely the highlights of the game. The best parts of Kingdom Hearts are always occurring in original worlds. KH tends to throw a lot of plot at the player at the beginning, middle, and end with Disney filler between. Organization XIII played a far less active role during the first half of the game than the villains did in the original, but their involvement kicked up a notch after the attack on Hollow Bastion.

As far as Sora's search for Riku, I never really got the impression that it ever really left his mind. As a keyblade master, Sora has a lot to take care of, and between fighting heartless and taking on the nobodies, it's not hard to believe that he'd get regularly sidetracked.