I think 1 and 2 should definitely be in the game. You could probably make an argument for option 2 actually being the default play. It would mean less micro and a faster pace to the game. As an option though it is great.
3 is a harder one to predict, especially on smaller maps with less power points, in those cases it would effectively act like a unit cap. Well, that is if you take away the logistics buildings too.
I liked in TA that you could disallow certain units/buildings or limit them. The people I played with were not fans of things like nukes and lots of Big Berthas etc. so being able to switch them off was great. Seems you won't have the big guns in this game though so perhaps not such a crucial feature.
Being able to select AI difficulty independently is good too, so one hard one medium, that kind of thing. Setting fixed alliances before the game starts, being allowed to ally with AI etc. should all be in there.
In Supcom 2 you could set different income and other bonuses to the AI too, like a custom difficulty which was pretty cool. I think in Supcom 1 you could also set the AIs preferences in terms of land, sea or air which was sometimes interesting. Though other traits might be more interesting like an aggressive AI, a risk taker AI, a slow but steady AI, a defensive AI etc. may be more interesting.
" You need radioactives to provide local power to more advanced units and buildings. " I am not sure if this is what you mean by local but it might be interesting if this or another resource could only be developed and used in that zone. If that were the case people would probably build bases or defence structures around them which on larger maps could bring in new strategic implications and just be pretty cool I think. I've always liked the idea of forward bases or region bases but most rts games don't have the scale for that so only really require you to have one big base and everything comes out of that. PA is actually an one of the exceptions to that where building factories etc. in many different places is very useful.