While you're suggestions are better than fanon, both of those ships really only appeared in Star Wars: Rebellion. We ran into the same problem with Empire at War only ships, and while we did use some of them, it was typically only for minor roles like scout and siege frigates that didn't have good equivalent in the Star Wars universe anyways. The Bothan Assault Cruiser is has a far bigger presence in the expanded universe, so I'm willing to fudge the dates a little in order for it to appear. Besides, with Rebellion we will probably end up giving player the choice to go later into the GCW than we do currently.
Yeah, that is the thing with the GCW, the Alliance Fleet is a mess, in particular Mon Calamari ships.
What ships are currently filling what roles for the Alliance? I already pointed out the minor Venator/Victory mixup in the Imperial capital ship roster, so the Alliance roster shouldn't be that difficult. I would personally suggest something to the effect of the MC90 be the battleship, the MC80 Home One be the carrier, the MC80a be the colony capital ship, the MC80 Reef Home (the wingless Liberty that you call Liberty) be the support ship, and the MC80 Liberty (what you call Maria) to be the heavy assault ship. I would reserve the Bulwark-class battlecruiser for the Titan role. The Alliance capital ship roster you have right now is just downright weird to me.
The thing about Empire at War is something very weird happened during development, many ships and vehicles that were already in the EU, like the Carrack-class light cruiser, the Assault Frigate Mk. I, and the 1M Imperial-class medium tank were going to be in, before suddenly being replaced by the Tartan-class patrol cruiser, the Assault Frigate Mk. II, and the 2M Saber-class repulsor tank, respectively.
You didn't sound harsh at all, I tend to use "fair" or "fair enough" as one-liner responses a lot. For SoGE, the GCI have been entirely ignored, there's more than enough content in the movies, novels, comics, and games to make up the ship roster for the Reps. The CGI is a pathetic joke. Imho when it comes to TV, the short cartoon series was quite a step up from the CGI, even if it wasn't the greatest.
Well, if Clone Wars era ships are ever need, and something can't be found in the existing movie/novel tech, then TCW is a decent choice.
When it comes to SW and Sins, I believe that star bases/stations are the real big issue, as in SW there aren't really stations that can take on and engage multiple Star Destroyers with ease. This was something seen in EaW, where entirely new stations were thought up for the game.
The EaW stations/starbases were pretty bad, though the Cardan-class space station series is fairly believable, but the Alliance space station is just weird. The Golan series space defense platforms are the only real stations that could combat Star Destroyers.