You know how the Covenant do not really understand/make optimal use of Forerunner technology, usually ending up with pale imitations and innovating slowly? And how in First Strike I think, Cortana altered a captured Covenant vessel's remaining plasma weaponry to turn them into far more potent weapons to better bring out the limited potential of their ship design?
Perhaps UNSC captured Covenant vessels could be improved under the powers of that faction. By this I mean, the power in the game is a team of spartans capture a ship and upload an AI. Well, would it be possible for that AI to also improve the capability of that ship in any way? I am not saying majorly at all such as drastically altering the weapons (and I have no idea how that would even work in the game engine), but maybe just slightly improved shields, slightly improved speed, and/or slightly improved weapons. Come to think of it, maybe the only reason Cortana was able to do that was due to her time spent in Forerunner constructs, and that springs to mind maybe a later game research option. Just a thought.
EDIT: So apparently I am wrong, it has a long while since I read the books and I could have swore there was something about AIs bringing the fuller potential of Covenant designs in them somewhere.