I agree with you that Ribery was way over-valued in the summer transfer window last year, but I think Bayern just said this (that he was worth more than Ronaldo and Kaka) to make Ribery stay because it was too much money for the others to pay. Or if Real Madrid was stupid enough to pay Bayern would have gladly take it. But in the end I think they were happy that Ribery stayed because as we saw in these 2 games vs Man Utd they can finally contend in the Champions League with world class players such as Ribery and Robben, without forgetting Schweinsteiger and van Bommel in their midfield. It must be said that with Robben arrival last year, Ribery lost a bit of importance in their attacking options, or maybe now the creativity on offense is shared with Robben.
As for the game yesterday, you're right, Rafael played an excellent 1st half but really it was not that difficult given how Ribery played this 1st half, not able to do anything on offense and not coming back to help his team in defence that's why Rafael was able to make runs as you said. I was disappointed by Ribery's contribution in this 1st half. All that changed in the 2nd half, where he seemed much more motivated and Rafael started to have problems containing him. I also agree with you, it wasn't a nasty foul on the 2nd yellow, but in my opinion this kind of foul where the defender really doesn't try to play the ball to prevent a dangerous action from the other team should be a yellow, plus Ribery had the ball inside the Man Utd half, Rafael should have known better even if he's young.
I know Man Utd is not a one-man-team, but Ferguson starting Rooney proves he doesn't fully trust the other players at his disposal like Berbatov or Macheda. And yesterday I really think your team got tired from the time Rooney started to hobble on the pitch at the end of the 1st Half, even though he is a special player he can't do much when he is injured. I thought Rooney would then be replaced much sooner as I think Man Utd let a lot of energy with Rooney walking on the pitch for a long time.
Good luck the rest of the season!