I second this. I've gone back and forth between the vanilla CM9 build and the Samsung touchwiz on my Galazy S2. While the CM9 feels faster and cleaner, it's all lacks some key features. For example the vanilla music player doesn't support displaying ID3 MP3 lyrics, a feature my windows mobile phone could do back in 2003. This feature is critical for podcast courses with embedded lecture notes. And yes, the widgets work better in touchwiz too. In the end, I always go back to the more feature complete touchwiz.
Touchwiz is definitely the 'last worst' of the Androids and some of the feature tweaks are/were definite improvements.
Having said that I've got a fairly close to vanilla Jelly Bean on my SGSII now and I can't think of anything I miss from stock.
After 60 seconds of looking at it they both admitted that the thing I was moaning about was horrible but that it wasn't something they had to deal with on their Galaxy S3s. When they showed me the S3 it's mechanism was definitely more intuitive (at least to the three of us).
While I'm not defending the skinning efforts of OEMs generally, I don't think the historical position of "it's all awful" is necessarily true any more. Sure there are bad things in there but there were plenty of bad things in early versions of Android. Just as Google learned there are signs that the OEMs are learning too.