If I might make a suggestion for this?
Advancing time. Sure, one can enter a stable orbit, and hold shift, but that takes about 5 seconds per day! Waiting three minutes for a month to tick on by can really add up.
Primary things I want this to accomplish: Time out, and bring in new bounties; Restock stations; Replenish defense fleets, and hurry build times.
Mind you, I haven't a clue how this would affect the game or AI, especially given how there's a loadingscreen at the start of a new game that's advancing time
I'll look into it, but I wouldn't get my hopes up if I were you. I'm 99% certain mods can't mess with the game's timescale the way the new game advance can.
Will it be possible to add & remove features from planets going forward? Ie, remove trace ore deposits, add rich ore deposits etc..
Adding/removing conditions is absolutely on my to-do list.
Also is it possible to increase the structure cap from 9 per planet? Would a slider appear if so?
From what I've overheard on the Discord, the structure cap is currently hardcoded to 12. Sorry about that!
Not sure what Im doing wrong (if I am doing anything wrong that is) but when I run the settings command and try to make it to where all the ships and stuff gets sent to my "Home" planet, its kinda darkened and I cant toggle it, I used the sethome one to set my home to one of my colonies, but it still wont work. What should I do or is it an issue with the .9a dev version of CC?
That setting isn't implemented yet, hence why it's grayed out. It's been on my to-do list for a while, so I'll try to get it in for the next release.

Perhaps I'm in the minority here but I feel the 'God' command should be a blanket command for infinite ammo/cr/flux. I mean, if you're flipping on the invincibility, you'd may as well have the rest of the effects.
At its core the console is a mod testing tool, and God is meant to test a ship's weapons/stats in combat without worrying about it dying. Infinite flux and ammo would detract from that.
That said, there is the alias 'tc' (short for "toggle cheats") that activates god, infiniteflux, infiniteammo, and reveal in one command. You can use "list aliases" to see the full list of aliases (and aliases will be editable in-game soon).