I think the most worthwhile changes to Anaxes would be a complete rework of the Navy area, it is far too big for what's there and as such, is generally underutilised, perhaps the majority of it could be removed while the access point is changed to being solely the Navy area in the hangar. If this was changed, that would leave just R-Sec on the third floor. The third floor could be removed entirely by changing the location of the citadel and putting R-Sec there instead. The side hangar seems fairly useless, it is almost never used for anything other than training so that could probably be repurposed. The training areas are fairly far apart which is quite annoying, you could put a few training areas and a citadel under the map somewhere and used timed elevators to access them. This would open up another area on the second floor by getting rid of the primary training room, this could potentially be turned into a high command area. The stairs leading to the upper floors are also a pain and not very reminiscent of Star Wars, they could be replaced with timed teleport elevators. The primary hallway materials make me feel like I'm in a hospital and could be replaced with something a bit more Clone Wars-esque.
Exterior is pretty accurate right now, although the tower did have turrets on them which could be a cool addition if you made the functional.
Adding this reactor would be pretty cool but would take up a lot of area and not have enough functionality to be worth it. We used a nearly identical reactor for the Coruscant Base and I think Shy published the models he used for it.
A 3D skybox would also be epic