The factory scene is quite terrible for many reasons, but the droid stuff is the worst part within. Without it, it’s just a dumb action scene that serves as a transition from “our heroes walk in the bad guys lair” to “oh, now they are in big trouble !”. Not pointless, just… not very good.

As for Yoda’s fighting in RotS, he doesn’t jump like Sonic anymore, so the scene is better (and besides it has a symbolic value which is almost none existant in AotC). The most terrible sequence for me in RotS is the scene where Anakin makes his choice, especially the lightning part with the melting face. I like the movie as a whole, but this sequence was so embarrassing… (thanks to fanedited versions for having that corrected in a way I’m more at peace with now).