I have the feeling that I'm the only one who actually likes time travel in Kingdom Hearts.   
Things that I'd change: 
  
 - Kairi needs a little more character development 
 - Same goes for Namine 
 - Yen Sid's "story" should be explained (Is he a Keyblade master? How did he teach Mickey?) 
 - I would remove some of the "goofiness" (pun intended) of the Disney characters 
 - More interaction between Sora and Roxas (Like in the Re:Coded movie) 
 - The original story should be distributed more evenly, not 90% in the beginning/end (People will continue playing) 
 - Maybe explain some plotholes though some of the fantasy/mystery could get lost 
  
Design wise:  
  
 - Sora's default face