Im just waiting for the day there is hard proof in super that GT doesnt exist or cant. People say SSJB is proof of that but i dont know.. BS can be strong in DB and goku and vegeta could lose his power. Just need something solid... come on Super don't let me down. Also i like the new sayians designs and hope they make it into the game.
The major one is power scaling, which while inconsistent in Super itself the Super characters are way beyond anything seen in GT outside of maybe Omega Shenron and Gogeta which Omega Shenron was only STATED to have the ability to destroy the universe (we never see him actually do it). Characters in Super have been shown repeatedly, including Goku himself, to have the poewr to destroy the universe. SSJGod Goku is already stronger than the highest level of what's presented in GT, and Goku has already gone beyond SSJGod with the Blue form and the other shit he's been doing with it like Kaikon (and the "Mastered SSJ Blue" seen in the manga).
Characters in GT are constantly compared to Majin Boo throughout the series. It's also heavily implied that Majin Boo was the last major enemy they fought. End of Z sort of implies this, but it's weirdness is more along the lines of Goku being interested in Oob's power being similar to Majin Boo despite Boo being relatively weak compared to the likes of Beerus and other Super characters.
There's also the child Pilaf gang, as well as the fact that Kaioshin and Kibito split in Super.
The depiction and role of Hell is also drastically different. In Super, it's directly stated (as well as implied in the original manga and anime series) that Hell's purpose is to "purify" one's soul, and that Freeza's soul is so evil he's still in Hell. This implies other villains were "purified" which directly contradicts the depiction of Hell in the Z filler as well as GT. In Z Filler and GT, Hell is more of a prison rather than a way to purify the soul. Also, Freeza did not use Golden form in Hell in GT, despite doing it in Super after he broke out of the cocoon when facing off against Goku.
Pan has also been shown in both Super and End of Z to be more powerful than Goku and Gohan ever was at her age. in GT...Pan does jack shit.
There's other things but these are the main ones.