Bob, I have a new idea for your edit that could help you bonding even more in bonding Anakin and Obiwan as friends and workteam. It's a little invasive in the plot and would require some reference in the crawl, and editing both in ROTS as in an AOTC future edit. The changes needed are rather simple, easily doable and minimal, Vaderios could garantee so. There's also a nice moral question that would be left in the air at the end of AOTC.
Resuming, the idea is: Not all the Jedi agree in joining the clone wars as generals. There's a faction led by Mace windu who don't join the grand army after Geonosis. Though there's never actually a break-up within the order, there are disagreements in what to do.
Mace Windu and co. reject joining the war, and want to keep an eye on the senate (erase yoda's dialogue in the council season where they decide throw down palpatin from office) and act on their own when they go to arrest palpatine. As Windu never directly serve palpatine's manipulative objective, there's a new taste for palpatine in killing him the way he did, isn't it?
Yoda, Anakin, ObiWan and KiAdiMundi (the latter just because his protagonism in order 66 sequence) join the army, and usually go abroad.
This way you would be establishing:
a) Anakin/Vader's passion for military operations
b) Anakin and ObiWan being in some way separated from the "rest" of the Jedi, which would make them be more tied for the spectator, as I said, they would be in a way, the Lennon/McCartneys of the order. (you could chain this with other ideas I had about how to bond them in order to have a far more character-centred movie)
c) THE MORAL ISSUE at the end of AOTC regarding the Jedi should fight or stand for peace.
d) THE MORAL ISSUE in the OT of having Vader, ObiWan, and Yoda be responsible of fixing what their former actions did.
As usual, a long post for a rather simple idea. Bob, I have been making some mp3's about the proposed dialogue for the scenes. 3 changes would set this subplot, 2 of them are in ROTS, so if you are interested in this, let me know and I'll PM you.
Cheers, and sorry for the dense post