I like the thought of being able to link resources on islands to cities without fiddling about with boats, although ideally that could be done way before genetic era... maybe a modified worker with amphibious capabilities? Expensive to maintain/build, so you'd just use it to set up connections and then *poof*. For example, if i play the romans, i have islands in my radius that are very awkward to mine, and simulating the east indies company's exploitation of the indonesian area is very difficult.
I think the sea based cities are wonderful but omigod does it place a lot of strain on my old pc, using up the sea for cities means that the resource load increases immensely.
Some of the units seem out of whack; for example the cyborg was a big leap up from tank (i think it has an attack of 50?). Some rebalancing would be good. Being a cyborg doesn't make you super, except in comic books. Having built in GPS, infrared vision, and slightly increased strength and speed is feasible. Robotic troops would make more sense as very tough units, and that is pretty much the direction the US army is going at the moment. They are unlikely to look humanoid. I think they have already been used to kill someone (memory hazy). At the very least, remote controlled killing machines are being worked on, and the goal is to make self controlled units, although i hate to think of the consequences of a bug meaning that they slaughter all the humans, not just the enemy. And if they self replicate, then I would say we are doomed as a species.