RATM

Rear Admiral
This mission has you destroying the asteroid base with the victory in tow. At the end of the mission you rejoin the destroyers. That being said, the destroyers don't come with you to destroy the base which makes a whole lot more sense than throwing a carrier at it. Was it engine limitations?

With these tactics there's no wonder we're losing the war!
 
That would make sense, I mean one of the destroyers can guard the Victory (after all, she is not that far behind and also she has fighter escorts, so she is not helpless), so the other can come with you.
 
This mission has you destroying the asteroid base with the victory in tow. At the end of the mission you rejoin the destroyers. That being said, the destroyers don't come with you to destroy the base which makes a whole lot more sense than throwing a carrier at it. Was it engine limitations?

With these tactics there's no wonder we're losing the war!

Interesting point. Yes it could be close to the engine limit. Way back I remember using HCl's WC3 mission creator and I think there was a limit of ten ships per nav point at a time. You could get away with one or two more above that, but it would be prone to crashing and dumping you into DOS with message - "too many watchers".

So I guess with Blair, wingman, Victory and asteroid base you already have four, add in a couple of destroyers and there'd only be room for four enemies. Although I could be wrong about 10 being the number.

TLDR: I think you're right about it being WC3's own limits.
 
It is the same reason that the Victory suddenly has no escorts when being attacked, or when escorting the Behemoth. The game cannot handle it.

While I am not a big fan of WCP story-wise, it is the only WC engine which can somewhat do justice of the actual game universe. If someone were to lift these restrictions without crashing the game or introducing problems, I would be glad to start designing an enhanced version of the game's missions. The Wing Commander III Enhanced patch is almost there. Plus, we (or rather I, right?) would need a better editor.