It may not have the CIV2 scenario editor (which is bugged and crap anyhow),
And it may be harder to implement certain things,
But I think ToT is the most superior of the CIV series.
It is held back by the poor animation graphics, but it has more
events, better rules options, and if you disable the sprites, it
opens the door to far better looking graphics, with a bit of work.
I think it is trickier to create scenarios on ToT and this has reduced
it's popularity, but with a bit of work, you can do wonders!