One thing I've noticed is that Green always has water and Blue always has mountains

Personally I could see this being a good thing, giving you two different play styles to choose from.

But from my personal experience, it's harder to actually breech a good defense on a water way than it is to breech inland. On Blue's side I would borrow for a few minutes to their spawn and pop out little bunkers every here and there, and like a prairie dog I would pop my head out, shoot 1-2 people, pop back in and do it again from one of my multiple holes. If I died, all I had to do was get across water (which sometimes can be difficult if your team hasn't secured a path) and get into my little hole and walk my way back to my little tunnels.

Its far harder to do this on blue since they will most of the time not have a lot of land to dig into.

It would be nice to see if map generation could select if water was balanced, or towards a particular side.

(also change water jump, crouching at the top is easy but annoying for newer people)

As a blue-only player I can say that on most maps a good blue team will build bridges to speed up Spawn - Frontline transit. If the green team is smart they will smash down the bridge support.