Nemesis had great potential.
The clone infiltrator plot should have been larger. The current Captain of the USS Titan is a clone and the Enterprise has to fight against a Federation starship. And they should have dumped that silly B4 sideplot. It wasn't necessary at all, it was a waste of precious screentime.
Spock should have had a role in this. They could have at least
I'd have left out the Reman subplot. Just have a Picard clone work in Romulan mines, amongst convicted Romulan and interspecies criminals.
And Worf should have gotten a major, well choreographed, epic fight scene (finally). Worf in a big blade fight/fist fight against badass Ron Perlman.
And then, and while it sounds minor it's actually a huge change: have the drydock scene at the beginning, and have the wedding at the END of the movie. The relationship between Riker and Troi came out of nowhere. It would have been nice and would have made for greater drama to build up to the wedding during the movie. And a "Picard gets orders, Enterprise triumphantly leaves drydock" beginning would have been a great nod to TMP, and they could have finally shown the Enterprise-E in all her glory in drydock.