I had the chance to sit down and try most of these things out this morning.

The Mace Windu dialogue thing sounds good on paper, though removing it leaves a pretty noticeable continuity error. Sadly, this doesn't look good enough in practice to actually do.

Dooku's death... I'm indecisive about it. I went ahead and edited it the way it was, without Palpatine ordering Anakin to kill him, but made it last as long as possible. When I watched my own edit of Ep3 with friends, I thought the moment went by awfully quickly.
When Anakin kills Dooku on his own, it characterizes him. He's been affected by the Clone Wars. He has become powerful enough to overcome Dooku, and ruthless enough to follow through on it, only reflecting on it afterwards.

Keeping the events as they are in ROTS, it characterizes Palpatine instead, making Anakin less strong of a character. At least at this point, I feel better erring on the side of removing Palpatine's goading.

EDIT: Plus, it makes the act of killing Dooku the result of anger and tapping into the dark side, rather than obeying the Chancellor after he'd calmed down.