Capital Ships

Thats is pretty easy if you want to learn to mod. Just go into the 3 player entity files and remove the frigates and cruiser and set count to 0, remove frigate factory and -1 of the structures count. If you want more detail, remove the research lines for cruisers and frigates.

http://soase.weebly.com/modding.html

Okay, that is simple enough I suppose.

I guess what I'm looking for though is something (and I hate using this as an example, but it's the first thing that pops into my head) like the "invasion" force that the aliens used in Independence Day.  This is the "structure" of your force:

"Mothership" (your transport to gravity wells)

A huge ship (like executor size) that is primarily for transporting and repairing your armada.  Has minor ship building abilities.

"Capital Ships" (transported to gravity wells by the "Mothership")

Large ships that serve two major roles; taking out structures and defenses, and being your "ground" assault.

"Strike Craft" (used by your capital ships)

These basically provide support for your ground forces and as well defend the capitals from other strike craft.

It would be interesting because this would make it to where you can really only try to conquer a planet one at a time and make your starbases and other defenses much more valuable.  You could even make it to where there is like two "gravity wells" (maybe, probably depends on coding), layer one for your motherships and capital ships, layer two for your capital ships and strike craft.

What I mean by the double gravity well is that you need the mothership to transport the capital ships, then you need your capital ships to transport your strike craft.

Let me know if there is anything like this currently, if not, maybe we could get a team together to get something like this to get it started?

You cannot dock Capitals. Only Strike Craft, cargo ships can dock. Code limitations. 

Might be some others wishing to help your project but I currently have like 20 projects on the go for this game alone. I will try and point you in the right direction though. Good luck and welcome to the mod community.

Could you give Capital ships the dock ability?  Or make a Strike Craft/Cargo Ship into a capital ship?

No

You might be able to make Capitals into strike craft.

You would lose any and all experience abilities when you do that.

Individual fighters dock. It's kind of interesting to watch. But you would need to reduce the squad size down to 1, just for your information.

You would also lose shields and shield mitigation if frigates or capitalships were converted to squads. Also a lot of abilities would no longer work IIRC.