There was a recent thread on ProgressiveEars.com about the later Yes albums and I thought it would be interesting to summarise the views therein. I found 36 posts where I could derive someone's rank ordering of albums. I then used sequential STV to produce an overall result. And the final top 5 are...
1. Big Generator
2. Keys to Ascension 2
4. Fly from Here
5. Keys to Ascension
Which I thought was rather interesting. The period after 90125 has so many varieties of Yes: there was YesWest vs. ABWH plus the hybrid Union. Then came the classic line-up of reunion of the late 1990s, with and then without Wakeman. Finally there's the post-Anderson era.
And each of those very different Yeses gets into the top 4: Big Generator for YesWest, Keys 2 for the classic reunion, Magnification for the classic line-up minus Wakeman and experimenting with an orchestra, and Fly from Here to represent the Yes after 2008. If you include Billy Sherwood's role on Keys 2, you've got most of the people who've been in later Yes included (no Davison yet, no Khoroshev). You've got more pop-oriented music, retro prog and attempts at something new.
What's made later Yes work hasn't been some simple line-up combination or particular direction. Later Yes has blossomed in unexpected ways.