I completely agree with your first paragraph, NTJedi. I'll be disappointed if water doesn't allow for at least that much.
On the topic of underwater cities, I agree they'd be cool but they wouldn't really make sense. The two playable races are humans and human-derivative Fallen, neither of which live or even can live under water... I guess you could make it work through magic but it seems a little excessive to me. On the other hand I'd love it if they design waters keeping underwater cities in mind, so that they can be added in later on by an expansion or mods.
Battles on water can then take place on the deck of two ships which meet.
I actually really hope they don't do this (and as of Stardock's last comment on this matter, water battles will be auto-resolved). The reason is, if I have an army of 5000 soldiers, some of whom may even be mounted, they really aren't all going to fit onto the decks of two ships. Not to mention I wouldn't want to be riding a horse on a ship (bears are more stable though, so that wouldn't be so bad
).
I'm not too bummed that they aren't planning on having player-controlled naval combat, but I would definitely be excited if they reverse that decision or if they add it in for an expansion.
I think the best way to do player-controlled naval combat would be to have the players control their individual ships. Flying and swimming units would also be able to participate directly in combat. Maybe ranged units could, too. There could be multiple ways of defeating enemy ships:
1) You could immobilize ships with sails by doing enough damage (think taking out the mast)
2) You could physically destroy it (most easily accomplished via warships, magic and large powerful creatures)
3) You could disable it by killing its crew. Ranged, flying and some sea creatures, as well as magic and onboard armaments would help here. Also, it could be possible to simulate boarding other ships, in which case melee units would also contribute.
In the case of melee and ranged units contributing to such naval battles I think it'd be best if, rather than acting is individual units they simply contribute to ranged and boarding strength stats, abstracting away that level of detail for the sake of practicality.
Nonetheless, I could easily see a system like this becoming very unwieldy once fleets get big enough. For one, you'd have to choose how to distribute your forces across your fleet, which could be very tiresome. Secondly, if you control individual ships, well, things would get chaotic once fleet sizes start heading upwards of a couple dozen ships. So basically, I'm not holding my breath for naval combat.