Two comments:
First, perhaps in in hindsight I should have limited retrotech to 3 or 4 levels. Or not, I could argue both sides... especially when you bring in comparable robot brains.
Second, ship computers are not explicitly covered by retrotech. Core, especially, is like the nervous system of the ship, not just a brain, not just a CPU but also communications, panels, and interfaces, so at the very least, you should consider the Ship's Brains rules from the Robot Handbook (p.102) - and if those rules are in conflict, then that's on me, since I did both the CSC update and the Robots book.
I an honored by your response- I did not expect the author to respond.
Yes, Ship's computers are not explicitly called out. The greatest limiting factor for retrotech ship's computers is the restriction that you can only have one in operation at any given time. I run a lot of scientific games, and only Core's have the processing power to run the software required (Some of the software is 30+ BW). They are just ridiculously expensive.
Using the Robot Handbook, it is possible to create a fairly significant option using the Ship's Brains and Vehicle Brains rules. I had not considered "removing" the ship's brain interface functions from a regular ship's computer; that just does not seem cost effective. For replacing virtual crew members, Ship's Brains are much more efficient (even if you have to place multiples on the ship- similar to Rio's virtual crewmembers on la Sirenna)
Funny you mention robot brains- I started replacing "Computer Weaves" and "Intelligent Weapon" with Hunter/Killer microbots with zero-slot options. Nothing quite like having combat armor that recognizes a threat, and then acts accordingly
Granted, I have an evil purpose, because I also aggressively address the hacking of these types of systems (Thank you Blake's 7, I, Robot, Battlestar Galactica, Andromeda, ST: Picard, etc) for highlighting the dangers of over-automation, computer networking and AI in general.
As it sits, I have a neat adversary whose clothing has microbots with a habit of accessing intelligent weapons (and computer weaves and neural implants), and then forcing them to crash (or misidentify IFF tags or transport you to a hellish VR nightmare). Onboard his ship, the Ship's Brain has an even greater capability (since every square mm of the vessel is under constant datalink).
Low-tech guys with dumb revolvers, swords and good-old fashioned armor can waltz right through. Corrupted Battledress has a habit of replacing the inside atmosphere with carbon monoxide...