The only one where I felt any scene was put in just to be there was ROTK, and even then the EE was much better than the theatrical. Two Towers was actually the worst of the 3 in theaters, but its the best of the 3 in the EE.

What I did with the side changes, I took each disc, shrank them with DVDShrink, combined them, and now I have each one on one disc. These, though, are the ones I'll watch when I just want to watch them for convenience - they only have the video and the Dolby 5.1 track. If I want to watch them for quality, I'll watch the "official" ones with DTS and a side-change.