I think Nemesis is...fine. I bashed it when all I had seen were snippets and knew the plot. "Clones??? CMON!" But once I saw the whole thing, I think it's 'badness' is overrated.
Though I would:
Replace B4 with Lore (requiring massive changes of course, and the end isn't that Data is in Lore, but rather that Lore is shaken enough by Data's death that he rethinks his path)
Remove the dune buggy scene.
Add back in a lot of the character stuff that got cut.