I don't think there's a single reason. The changes are different in its intentions.

For some, like putting Hayden as Anakin in ROTJ, it's obviously to connect the two trilogies. In an ideal world, he would have made the prequels more like the OT, but he didn't, and know to try to connect them he puts prequel shit in the OT. If you watch ROTS and Star Wars back to back you can see they really don't work at all, Lucas probably notices this and adds more and more crap. Also he probably thinks the prequels were good movies and sees nothing wrong with adding more stuff from them.

The NOOOOOOOOOOOOOOOO!!!! in Jedi was probably Lucas feeling pretentious (like when he goes on and on about themes and myths instead of telling the truth that he started with the intention of basically making a comic book movie) and he came up with more "poetry" and "rhymes" and "mirrors. Whatever.

And seriously I wouldn't be surprised if some stuff like the rocks covering R2 is some jerk who works at Lucasfilm who says "You know George, it's very stupid that the Sandpeople don't notice R2, we should cover him with rocks! I can make it in an hour". And Lucas, who judging by the awful color timing he approved, doesn't care anymore and just goes "OK". It doesn't matter to him anymore that R2 couldn't get in and out of those rocks, just like when he was presented the design for the Jedi fighter and R2 could fit in there with a little bit of cheating. He doesn't care and has surrounded himself with a lot of idiots.

Who knows, maybe Lucas actually restrains some of the "computer people" at Lucasfilm, perhaps someone has already suggested to replace Yoda with CGI, only to be hold off by Lucas.