If I could remove one thing from Dragon Ball GT, it would probably be the concept of trying to recapture the original Dragon Ball magic. Shrinking Goku down to a child from a dumbass wish (and then plot-haxing it out with Super Saiyan 4) and chasing after the Dragon Balls couldn't possibly mimic that kind of nostalgia after everything introduced in Z and even the latter portion of DB. You had guys that could destroy universes as opposed to people that were impressed by elbowing a brick wall into oblivion; there was no going back to that as far as a sequel went. If they had simply made an off-shoot one-shot type of series with different characters, maybe, but not after Freeza, Cell, and Majin Boo.
I've lost my train of thought, but yeah, get rid of the nostalgia trip of adventuring for the Dragon Balls and replace it with a more straightforward Tenkaichi Budokai style tournament with no cop-out endings or interruptions. You could still bring in more of the universe by holding the tournament somewhere else in the galaxy so Earth wouldn't be in danger.