I have been playing with TBM/VEM from almost the moment CivV came out, and now that I have G&K I have played vanilla for the first time ever.
To my surprise, I find the vanilla game excellent. Lots of Thal's most important changes have now been incorporated into the base game, the AI is much improved and naval combat now exists. Three things in particular have struck me:
* cities are now much harder to take without combined arms and catapults (which no longer require iron!) are necessary to take cities (and not good for much else).
* Gold is now much more difficult to get in the early game, which adds challenge to fielding an army.
* Research Agreements seem to be fixed; and science is a lot slower than before.
In all, I would say that the devs learned a lot from Thal's VEM work, and took a lot of his ideas to make the game much better. To my surprise I am now considering NOT downloading the new CiVUP when it becomes compatible – although I must admit I really miss some of the UI improvements. The only thing that still annoys me from vanilla now is the 'full heal' promotion – that should really have been removed as per VEM.