Id like to see a game that occurs between OoT and TP that has gannon attack castle town with a huge army, this would explain why gannon is put on trial for execution as well as explain why the temple of time in TP is hidden in lost woods instead of castle town. gannon wouldnt have to be the main villan for that to happen, Majora for instance could be the main villan..Majora him/herself.

If you want to know more about what would be good in future zelda games theres another thread almost identical to this, "The perfect Zelda game, What would be in it?"