Stone,
I'm not the guy in charge of continuity and model inclusion, but let me see if I can answer your questions. Anyone on the team who knows otherwise could certainly correct me (wouldn't be the first time).

1.) I don't know that I've seen a Wraith model done by the team, but I think I may have seen a Gladius. As far as I know, there is no plan to include the Wraith (one of the reason's being is that it was a very rare and expensive fighter, and may have been in service mostly in secret ops, like in Armada).
2.) You will see Lexington class carriers, I can confirm that for sure.
3.) As far as I know, we don't currently have plans for unique paint jobs for different squadrons. I'm fairly certain that the FS2 engine allows for different squadron insignia, but I'm not sure if we have implemented that. I'm sure someone else can say for certain.
4.) As of now, we don't have autoslide in the mod. That is an interesting thread. I'll bring it to the team's attention.
5.) I don't know that we have done a Confed Command Base just yet, because I can't recall it showing up in any of our missions. Psych or Viper might be able to correct me if that is not the case.
6.) Also, I just wanted to make this clear, while you are free to ask us any questions you want, we may choose not to answer some, or not to answer some directly, because there are certain parts of Saga that we want to keep a surprise. I hope you can understand that and won't feel offended if that occurs with any of your questions.
I agree, though, that czacen's command base looks incredible. He is very talented!