Not one specific thing, but I'd change how Jar-Jar is handled.
Notably - when the bongo loses power in the planet's core, he'll actually get out through the person-permeable canopy to fix the damage, establishing him as mechanically competent and we know where he's coming from when he's curiously bumbling around the pod racers and droids on Tatooine later: he's someone trying to expand his knowledge and contribute his mechanical skills, not an ignoramus touching things he's absolutely clueless about. Having him get out also makes him a contributing member of the team, putting himself at risk to help the heroes succeed in the mission, instead of just being dead weight.
Also, while he's out there, he has a communicator to talk to the two still in the Bongo to coordinate repairs and restarting, and when he does, he speaks "Normally" instead of using the ousa/eesa speech pattern, indicating that the funny honking is a result of their anatomy not handling speech outside of aquatic environments all that well. When they DO restore power, and have the Big Goober Fish reveal, the following chase has more tension because Jar-Jar has to hang on outside the ship - the fish doesn't need to go through the ship to get him, and he could lose his grip.
Then, at the end of the movie, Boss Nass doesn't randomly promote Jar-Jar to general - he reinstates him as General, revealing that there's more to his past and character than we've seen.
In the final battle, Jar-Jar is more proactive and assertive, in control and confident in his commands, even though he's also clumsy and his orders aren't always apparently tactically sound. Of course, Roos Tarpals isn't completely confident in Jar-Jar's command in the final battle, and there's friction between them.
Most of the scenes in the fight are the same, but Jar-Jar's less of an idiot: in the scene where he gets his foot tangled in a bisected battle droid, we first see him dispatching another droid, THEN flailing about trying to get it off him while also fending off the advancing enemy. When he gets caught on the AAT, Roos tries to get him to jump to safety, but he demands a boomer instead - he intends to disable it, even if not QUITE as clumsily as he serendipitously managed to do so. He orders the retreat after the shield generators are destroyed, and deliberately opens the ammo cart... and then, at the end, he surrenders, and supplementary material can spell out that he did so to buy time for the others - it would take longer for the battle droids to figure out what to do with the surrendering Gungans than for them to stop chasing the retreating forces and killing the stragglers (And the Battle Droids DO accept the surrender despite orders not to because they're repurposed mall cops programmed to not commit warcrimes)
If you could change one thing about The Phantom Menace what would it be?