I don't think Obi-Wan needed Yoda's permission. Obi-Wan only says, "I took it upon myself to train Anakin..." If Yoda is missing, what is Obi-Wan to do but "take it upon himself." There is nothing implied in Obi-Wan's OT statements that he needed Yoda's permission.
Ep. II : Initiated the clones on Kamino and brought them over to Geonosis which essentially began the Clone Wars.
I don't see how it is necessary for Yoda to be the instigator of the Clones being utilized, in fact, it makes Yoda look like he's the one to blame for the entire "Clone War."
Ep. III : Was the voice of reason to Anakin before his fall. Fought the Emperor and was the one who commanded that the remaining Jedi go into hiding until the time was ripe.
Well, that I can't argue with. Yeah, Yoda is (or was suppose to be) the voice of wisdom--which no one heeded. But, again, I don't think it was entirely necessary for Yoda to confront the Emperor. It could be as simple as Yoda felt he wasn't physically strong enough to face the ultimate Sith, and that it would be better to train someone young and strong to do it. But, I guess it all boils down to preference and taste.
But, like I say, I wouldn't mind a knock-out, drag-out Force-fight between Yoda and the Emperor. The scenes in ROTS came close, but not close enough for me. There are kernels of little goodness in the giant dog turd, but I still wouldn't eat it....