The underwater cities which were promised were cut, and its been stated they will be in the next expansion. Theres other stuff too if you google it.
I don't personally remember Will Wright mentioning underwater cities in the videos we saw back then, but if he did it makes sense that something so large scale (and so different to the current game) would appear in an expansion. I wouldn't personally mind if underwater cities never made it in, because it doesn't fit.
Edit: I did some extensive Googling and it seems this was removed over a year ago, so why complain now? I also see nobody praising the fact that flying creatures were added, I think people are just trying to be negative.
The game as it stands now is very different from how it was first introduced many years back. At first your actions determined your genetic route - not simply placing things on your creature on a whim.
Your actions determine your gameplay now, have you not noticed on the creature history screen it shows if you've been "predatory, social or adaptable"? I've not gotten to the civilisation or space stages yet but I've heard that these behavioural branches determine what sort of empire you get in the end. I know for sure it affects your tribal stage because when I played an aggressively-behaving predator I got offensive skills like firebomb and some other thing.
I've been playing it all evening and while some of the phases are a bit on the underwhelming side (creature phase especially), the space phase more than makes up for this. Its great when you come across a planet colonised by creatures you created months ago with the creature creator. I've found some of mine in the creature, tribal and civ stages of evolution. Will be interesting to see if any have made it to the space stage yet.
I've actually been on the creature phase all day today, it's by far my favourite phase. I've met almost all species on the planet and have found all but one body part, that's how long I've been on it.

Speaking of finding your own creatures as well, I was shocked earlier to find a nest of my own species (the one I was playing at the time). It was genius, I could even mate with the lovey-dovey there and it even let me "migrate to" that nest so I would respawn there. So much you find out if you explore.
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