1. Plenty of old ships - Scims, Banshees, Epees, Bearcats, Ferrets, Avengers, the Intrepid, several Kilrathi ships and two or three old capships that appear only in cutscenes. And of course, the Bengal-class.
2. Just about, yes. For capships, and that includes Kilrathi capships, comm messages show a rotating logo of the faction that owns the ship (ie., BW logo for BW ships, Kat logo for Kilrathi ships, and Confed for Confed ships; bugs are the same as in WCP).
3. They do, but only if you fight well enough

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4. No ground missions. They're not really supported by SO, and though there are ways of simulating ground missions, they were only developed when we were about half-way through UE.
5. Most of the time, yes.
6. They appear a few missions after the start of the game.