No spoof movie in the past decade has entirely stuck to the genre it's set out to satire, so to expect that. For writers to limit themselves by not taking a swipe at popular movies for a couple of seconds out of a 90 minute movie, given it works, is silly. The spoofs outside of the genre were relevant to the scenes in the movie, so what's the harm?
..and I'm not going to "come to the rescue" of a movie I like, because I respect opinions (only when they have basis). Alyson on the "operating table", being pieced together a la Darth Vader? Would it had been as funny had it been Frankenstein? No. Pop culture, something people can relate to, is what's going to grab them. In fact, in Episode 3, I would have much rather seen Vader fall on his face from the tabel than stumble around crying, which was easily the most embarassing scene in the entire Star Wars franchise.
..and Tony Cox as Yoda? The underlying irony in that, and the basis for the Yoda quip, was that he was an Ewok in ROTJ, Battle for Endor, and The Ewok Adventure. The explanation is in the Director/Writer commentary on the DVD.
Oh, yeah, and he's small..like Yoda.