This whole thread is going to keep ME up at night!
I am positive you can delete spells, as you can totally change them around. The KingMaker makes good examples of this - and I am reasonably sure we can just delete the entire spellbook and start over if we wish (sadly, it would probably be best).
Watershape is in the next patch. We might actually see that patch sooner than later, if someone can get KO's attention to this thread, and he is in any way excited to see this project get rolling (who could resist this?!).
A note about terrain types, since it will be very important as far as the design of sites, and possibly some other effects -
Deep Water - Deep Space
Shallow Water - Near Space / Solar Space
Mountains - Asteroids / Dead Planets
Forests - Habitable Planets (Earth)
Grassland - Habitable Planets (Fully Terraformed Mars)
Swamps - Marginal Planetary Bodies (Partially Terraformed Mars)
Waste - Hostile Planetary Bodies (Venus, Jupiter)
I think because of how we need to think about distribution of terrain, that multi-province planets will be complicated. They'll be greatly restricted in terrain. I was sort of hoping that sites for Mountain/Swamp/Waste could be significantly different than those you would expect to find on an inhabited world. For example, a specific type of "Space Pirate Den" or something, that would only be found in Asteroid Belts, and never on an inhabited planet.
I'm starting to think that "Magic", the Sites and Spells, are going to take a massive amount of time and effort, and I'm thinking it's where I'm going to volunteer to start learning the modding commands, and how to build up these libraries.
I agree that everyone should get easy access to one type of gem, Earth is fine, it can represent Titanium or something, a somewhat common ore needed for starship hulls (and armored vehicles of all kinds). Each species of course would have a bit of a predilection towards one more more other types - say they have enormous Diamond deposits or something, so they get 5 Air/turn at their home, and a lot of Air summons.
I'll do some brainstorming after I grab some food, and see if I can come up with a preliminary list of actual gem types for discussion.