TV's Frink said:

I haven't thought this through very much, nor have I checked to see if this has been mentioned before...but would it be possible to completely remove Yoda from the prequels?

http://originaltrilogy.com/forum/topic.cfm/What-was-the-fatal-flaw-of-the-Prequels-if-you-think-they-sucked-aka-Lets-take-a-break-from-hating-on-the-blu-rays/post/536951/#TopicPost536951

Yoda isn't that important to TPM. I think he could be cut from that fairly easily.

In AOTC he doesn't do much important, and his scenes (younglings) could probably be cut easily, but he's IN a few scenes that are needed, so it might be tougher.

The entire Wookie planet sequence could be cut from ROTS no problem. It's the third act where he and Obi and Bail are together that would make removing him totally problematic.