Hull categories are a great addition! The hull list can get very difficult to navigate in lategame when you're fielding dozens of hull types.
Speaking of navigating lists, here's a suggestion for your consideration: One can type the first few letters of any name in the Economics, Naval or GU windows, and the game will select the matching population or fleet, which is very useful once you've got too many of them to count. However, this is impossible in windows where every item in the list has a prefix (in the Officer window, anything you can assign an officer to is prefixed with a required rank or admin rating, and in the Ship Combat window, every target is prefixed by its designated hull type) because the game will only search by the prefix, which is largely useless.
If the game could ignore the prefixes in these windows and search through the actual entity names (in case of assigning Ground Force commanders to GUs, I reckon ignoring both the rank and the GU abbreviation prefixes would be optimal), assigning officers to ships, populations and GUs and selecting targets in large naval engagements would be so much easier!
Another option I have considered is to have their ships launched from different bodies in the system, except for the orbital bases. In VB6, they used to have bases on multiple bodies with tracking stations and replacement ordnance.
I'm not sure how lore-friendly this approach to "Necrons" would be, but who cares? Having Precursors spawn throughout the system would be far more interesting than potentially never having to fight a single ship of theirs if you play carefully and station a large garrison on every ruin. It would also lead to very interesting multi-directional engagements. Although I think spawning their scout classes as a first wave a couple weeks or months in advance of the real awakening could be a good idea for large ruins, because getting overwhelmed by a massive fleet with no prior warning might be a bit too much.
There's also an option to spawn Precursor ships as wrecks that would reactivate upon salvage attempts or when the awakening comes, however this might actually provide too much information about the coming threat and make things too predictable. However, random derelict wrecks in general are something that's really missing from the game, in my opinion. We can already find ruins of clearly interstellar civilizations, with two or three systems having been colonized by the same race prior to its extinction, but there's not a single shipwreck to be found!
Maybe they've all been mopped up by the
Invaders (who are responsible for the downfall of all prior civilizations in the lore, if memory serves me right?) but it really doesn't have to be that way, encountering actual traces of the extinct empires' navies would add so much character to the game, not to mention interesting salvaging opportunities for the player or for the certain ever-ravenous spoiler.