Maybe it was coming from Civ4, Beyond the Sword, which made it feel empty in comparison, or maybe they've since fixed all the issues the vanilla game had at launch. I think most people's opinions of vanilla (mine included) were formed around launch, which frankly, was a huge disappointment.
On a tactical level, the AI was a complete joke, you could bug its troop movement by providing obstruction, and rather than simply kill your unit, they'd spend their turn reorganizing, over and over again while you pick them off.
Strategically, there... was little strategy. keep building cities until you win. The global happiness did not decentivise carpeting the map in as many cities as possible, as it was designed to do.
Also, every game saw ridiculous run-away civs (Ramkhamhaeng was a nightmare), which rendered games unwinnable from a very early point, as there were absolutely no counter-play mechanics available. Unless you were playing on very small maps with access to every competitor right from the start, on the other side of the world, someone had already essentially won the game, everything to follow just saw you waiting for the defeat screen.
In essence, there was clear potential, the game was just so horribly and unequivocally broken. I put it down until G&K came out. Even then I didn't consider it great, G&K just made it qualify as complete so far as I was concerned (also, Dido
).
Then comes Brave new World, which is not just a great game, but such a finely crafted "experience". Easily qualifying as one of the greatest games ever crafted so far as I'm concerned.
Looking back to vanilla is like looking into the dark ages, frankly I don't really understand why someone would choose to languish there.
It may be different now, but most of us moved onto the expansions as they came out, so we never had those bitter memories overwritten with anything better.