I'm thinking along the lines of orbital navy; frigates, destroyers, carriers and the like. The other thing would be space-stations, star-bases and deep-space-stations, constructable buildings that function similarly to a planet, in the idea that they have a gravity-well and can have units around them. NEW! In order to build carriers, frigates and destroyers, you must first build an advanced orbital factory. They could perhaps, if possible, have units dock until ready, healing them for a small energy and metal cost each, and while docked they always use up energy, but will use up personal energy reserves when ever they move or fight. Carriers have the most storage, fighters have the least. One more thing, the space-navy should be able to move 'freely' to any point in space, using gravity sling-shots if it is outside of their range; range can be decided later. Maybe if it works as a mod, if could be put into the main game? Thats my idea
Deep space combat won't work with the tools we have right now. Maybe it could be added down the line? But it would require a ton of work, if it's even possible. It simply may not be possible with the engine. What you're describing just sounds like a ton of micro...
Ok, one more idea i had, again i don't know if it is in already, but orbital fabricators should be able to build an Advance orbital contruction base that can in turn build frigates and the other vessels i came up with.