Modder brainstorming session

[Nitram Draw]

Nice idea. I think the AI would have a tough time handling it though. I tried a few games with colonize home planet type and atmosphere restrictions, this is as close as you can get to the few and far between colonizable planets now. The AI did not fare so well.
Making colonies more expensive is a good idea, they are basically throwaways as you put it. If you only have 10 each becomes much more valuable. Again, I think the AI would have trouble with fewer colonies and it isn't very efficient in picking colony types but in a game with human opponents it should work real well.
If the number of systems limit is lifted I don't see why most of your ideas cannot be used.