This version flows a lot better than before, I like it!
One thing that still feels odd is how short the scene of Padme and Nute is before the droids are disabled. Obviously you can’t include more from after that point, so the only other way I can see it working is to cut right from the surrender of the queen to the scene with Nute.
I just gave this a try, but it doesn’t really work. Cutting straight from Padmé’s capture to Padmé being taken before Nute just felt really off. And then it made the Qui-Gon/Maul/Obi-Wan scene feel like it lasted for ages. You could maybe expand the Padmé/Nute scene a little, and bastardise some dialogue: “Your little insurrection is at an end, your highness. Time for you to end this pointless debate.” But that doesn’t make much sense, or is a bit of a weird insult. (Maybe there are other options elsewhere?) You could end on the spare shot of Padmé staring blankly at Nute, but she’s got such a neutral face that you’d probably have to really spice up the music there to convey some emotion, which might also feel odd since we’re then cutting to the Maul/Obi-Wan fight, which has no music.
I do feel like it works as is though, even though it’s short. It’s a nice little gut punch that reminds us of why Maul needs to be stopped, that breaks the fight scenes nicely. In terms of our energy levels and interest, we want to get back to that tense fight quickly, I think?
On your other ideas, I think you should give them a shot! It’d be nice if Anakin flies into the control ship more deliberately.