It took me ages to realise you don't need water transport units to cross water! I think this is quite a good improvement, but perhaps my opinion will change as I play the game more. I don't like the inability to control research/culture/finance and I don't like the length of time it takes to construct buildings, most of which appear to have marginal impact. I do like the battle element which is much more realistic and has a less arbitrary outcome.
Yeah, took me ages to figure that out - I now have settlers going everywhere :-)
I though you could control the research / culture ... in each city you can change the priority, ok not quite as hands on as before.
Buildings do seem to take a while, unless you have decent industry around the city, tis a bit annoying - mostly annoying is the huge length of time it seems to build wonders.
The battles are much much better and do seem to make more sense, for once my tanks won't get beaten by a guy with a bow and arrow unless my tanks are several destroyed already.
I find the game still lacking something.... and yeah so far the last Civ is taking some beating but I do find the game is more transparent and I like the more apparentness of resources and the city states add a really nice dimension of trade etc.
I still prefer Colonization at the moment though.