Cutting the Gungan city is tempting for narrative speed but I think ultimately a streamlined version of it will serve the plot better - it will seem a lot better with Jar Jar & Nass dubbed or subbed (see BotF). Obviously only one "bigger fish" at most. The waterfall scene is both bad and pointless, it was well cut in the first place - I think some fan edits put it in just to seem different from the original.
Dooku in Ep I? I don't see how this won't seem tacked on, and distract from MTH's stand-alone ideal, which is a good one.
Maul = Grievous? No comment.
A special edition is a good idea, as it gives time to get one out, let the dust settle, and then be objective about what worked and what didn't.