Really? Do you have any examples? It's been confirmed by all involved with the project that no alternative vocals were used so I'd be interested to read which vocals you think have been replaced. Regarding instrumentation, I actually hear more stuff going on in the mixes, not less so, again, which parts do you think have been removed?
The funny thing is that it was exactly this topic that turned me off to the Hoffman forum when the boxsets came out. I remember people making huge lists of everything that was "wrong" with the new mixes. When some of them ventured over to the old genesis-music.com forum, I ignored those posts instantly.
Having said that, there were some curious developments on some of the songs when they went to remix them, namely, some of the masters couldn't be found. I remember reading an interview with Nick (it was either in one of the booklets of the boxsets or in a magazine interview - if we still had access to the old forum, I could find it for you in a heartbeat), and he said that when they were going to make a surround version of "Say It's Alright Joe", they couldn't find the original master. So, he had to use the best master at hand and create a "faux surround" mix - the amazing thing to me is that I sure as hell can't tell that SIAJ is not from the original master. It was very well done. Also, some others were never found in addition, e.g., the masters for the extended editions of "Mama" and "It's Gonna Get Better" they just couldn't locate; thus, they weren't included on the 1983 eponymous album's CD/SACD/DVD-A.
Just very recently, I finally upgraded my stereo to a surround sound system. And, since I also had a player that could play SACDs, I was quite happy to rediscover the boxsets (it really was like hearing them again for the first time). Unfortunately, there were a couple of bits that do, in fact, seem to be missing. Now, you are also completely correct that there are new things that were not audible before - I notice those on virtually every album (and they sound even more amazing in 5.1). The two albums that I pointed out early on as ones where I prefer an older version are the ones where things didn't sound quite right to my ears in the new stereo mix (those were "Duke" and "The Lamb").
So, since the new stereo versions were mix-downs from the surround mixes, I decided to check out the surround versions on SACD and DVD. I wasn't imagining things - the things I noticed were missing on the new stereo versions weren't in the surround mix either. Now, they are minor things - only two bits on "The Lamb" and a couple of more on Duke - but these things that I heard on the older stereo mixes are just not there. "The Lamb" ones I can remember off the top of my head, but the "Duke" ones I'd have to listen to again to get specifically (they consist of a couple pieces of piano accompaniment and a missing guitar break, as I remember).
The Lamb examples are the "la, la, la" bit after "she's such a fine dancer" on "The Supernatural Anaethetist" and a small percussion break during "The Colony Of Slippermen". In the first one, on the new stereo mix, you can still hear it, but it is much quieter than on the older versions. When I went to check it out on the surround mix, it is audible, but very faintly - the channel that usually carries the vocal track is the center channel, and, during the "la, la, la" section, it is completely quiet. Something happened here - I don't know what. The percussion bit in "Slippermen" is right before the lyric "he places the number into the tube" - Phil, on the older mixes plays, this slappy-sounding percussion part before the lyric; on the new remixes, it's just not there.
Now, that doesn't mean I can't listen to the new versions of "Duke" and "The Lamb" - I just regard them as new versions. As people have correctly said, there are many more new and extra things that are now audible on all the remixes of all the albums; however, there are a few rare bits from the original versions that are not audible anymore - thus, on two albums, I prefer the older stereo versions. However, overall, I fully embrace the boxsets and listen to them most often.