Flagship-support hierarchy: Has been commented on before. Personally, I'm not sure the devs can change that at this point, so it'll have to be relegated to the realm of (complex) modding.
Supports returning to carrier: They're support ships, not fighters. Of course, I do use small-size supports as 'fighters', but they don't really do... fighter stuff.
Static combat: Like the flagship-support hierarchy, this horse has been beaten before. Again, probably going to be left to modding.
Unique abilities: Well, the research-oriented patches a while ago added some nice stuff, and there's already a mod with more new toys. Not sure if the cloaking device and ECM/ECCM can be done within the current engine, though.
Unique aliens: This would take a bit of effort from either the devs or modders. I'm not sure if any more of that is in the cards right now.
Nebulae: I'm not sure we're going to see a 'Nebula' system, but if we did, I see no reason why it wouldn't have various special properties.
Custom shipsets: This one's tricky, IMHO. The devs have said they'd like to do something about that, but there's no telling if or when it'll happen. I haven't got a clue as to how to mod it in, either - but one workaround would be to just have lots of 'generic shipsets'. The Workshop already ups the shipset count to four. (Three as of the time of this posting, but I was trying to upload the Remnant shipset late last night, but it didn't work...)