Thanks for the feedback. I've told myself I've "locked" all three edits once I recorded the commentary tracks, though I've gone back a few times and re-edited them to match. Let me address your points in turn.
The "Weesa going' home" line seems fine to me in the context of this edit, just a short bit of non-slapstick silliness in the background. I did lower the volume on him as well. Also, one benefit of removing the entire underwater sequence from the first act is that Jar Jar is no longer banished. He's just a regular Gungan. Putting even an abbreviated version back in would require reintroducing this subplot. In my version, Jar Jar is just a regular guy and he's along for the ride. My motto for him was that he can stay as long as he behaves himself.
The podracing deleted bit was reincluded just so I could roughly recreate my musical score for the race the way I had years ago using DVD. Trust me, for V4 it won't even stand out as a deleted scene at all, with DrDre's upscaling job.
The end credits do indeed seem jagged. I applied some smoothing, though I just took a look in Compressor and will try a few test clips using stronger smoothing settings, and see if it makes a difference. If so, I'll reencode. If not, I'll release what I've already done so far.
You bring up a good point about Padme being cheerful in one scene, and annoyed later. However, she's talking to a small child in the first one, and even then she reads as unhappy to be there. She expressed disapproval with Qui-Gon the prior day, so it doesn't seem too inconsistent to me. I think, at the very least, the gain of improving Anakin's characterization as a great pilot outweighs the potential drawbacks. (Anakin is a great pilot, and Qui-Gon notices these personal things about him rather than taking a blood test.)
As far as the "this one's a decoy" scene, I agree that I like the part that I cut out. The reason is that I was using L8wrtr's idea of making Anakin the main hero of the end battle. Padme gets herself kidnapped, then Anakin blows up the ship, and then it's implied through editing that this is why the battle droids collapsed and allowed her to win. In TPM, Anakin's actions were seemingly redundant if Padme already captured the Viceroy and could put a gun to his head.
Lastly, I did remove one shot from the death of Maul, where Obi-Wan sails upward from the pit. I didn't want to cut it too short, either, though it is trimmed somewhat. It's a bit implausible regardless, I know.
So, I will see what I can do about the end credits. I do want to put the fan editing credits into the credits themselves, jarring speed or no. For one thing, I put a lot of work into redoing all of them so they'll look consistent, and it's the normal fan edit convention for these things. Harmy did what he did because he was restoring a film, rather than doing a fan edit.
Thanks for expressing your opinions about the edit. V4 is done, but any little things that can be tweaked without actually changing the A/V sync, I am still open to. :)