1. General Rild should have been as powerful as perfect Cell, not Majin Boo. That would have allowed Goku to fight him at SSJ without being his typically over-powered self.
2. Bra should've been a Super Saiyan right from the start of the story, no matter how much Vegeta may be wrapped around her finger I'm sure she would've got the same training.
3. Baby should've started relying on his own strength once he had reached maturity, instead of stealing people's bodies. He was supposed to be even stronger than Majin Boo but he certainly didn't live up to it.
4. On the subject of Baby; they should've played up his motivations more, to make him more of a sympathetic villian. The Saiyans destroyed his entire race, so he felt justified. But along the way Baby proved himself to be cowardly and a hypocrit, re-enacting the atrocities he blames on Goku. I could see maybe at the end he might come around and Goku would spare his life, so he could come back as an ally some day.
5. Keep SSJ4, but change its use to be more like Gohan's "ultimate" power up. It would allow Goku to use his full power again (At SSJ3) without the strain on his body, or the limitations of his child form.
6. Change the GT tournament completly, with some actual competitors. Goten, Trunks, Oob, Pan, Bra, Goku, and finish things off with a real fight between Goku and Vegeta, like they hinted at but cheated us on.
