Garvisus,
River: Leave it. Just block it with a Kraken similar to how you block the other passage ways between the starting areas with land units. That will eliminate the quick strike.
Big Water Body: I like it as it makes each starting area unique. The water doesn't give a defensive advantage at all. You can easily sail into anyone's lands on the water. Trust me I did.
Capitol City: I prefer to be able to make any unit in the capitol. It should be the one place you are unrestricted in case you absolutely need a unit and can't get it anywhere (Archon, Devil, Ghost or even a Kraken to control the seas etc). I understand if you want to eliminate the Crow / Eagle to prevent quick flying strikes and Gryphon to prevent easy neutral capture but just about everything else should be available in the capitol. I suggest you leave the Capitol income at the normal 80 gold.
Other Cities: They are severely restricted right now. A lot of starting spots totally can't get access at all to certain units until mid/late game. I worry that one decent hero stack will be unstoppable since there is virtually no access to Ghosts, Devils, Archons, Unicorns etc or even decent fighting units like Green Dragon, Spiders, Gryphons, WolfRiders,. The first strong hero stack may win the game as it did in my test game. I'm not suggesting adding a ton more production but opening it up a bit more would help even if it;s just 1 city that can make 3-4 good unit types so you have to chose what's important.
KGB