There are scenes where they need a CG Obi, esp the one mentioned in the last post note or Homing Beacon where it talks about a CG Obi jumping through the air & landing with his hood up, when they shot the landing of the jump his hood was down.... There are reasons besides armor for motion capture, Jango was filmed in armor, did you not see the 'Singing in the Rain' outtake?
The Jedi are the commanders of the clones......Right? So why would the clones who are expendable have armor and the Jedi who are most definitely not expendable not have armor? There are a lot of things that could happen on the battlefield that even a Jedi couldn't defend him/herself from. I think it would tie in nicely with the original Ralf Mcqarie painting of the Storm Troopers with shields and lightsabers.
I have to geek out and use the RPG defense here. In a role playing game, a character like a Jedi would not wear armor, as it would inhibit his movement too much and actually give him more penalties than bonuses. A jedi relies on movement and speed, so armor would just be dumb, unless you were one of those jacked up force users like Vader.