Honestly, I don't think it's fair to compare the space combat to anything - other than what I imagine space combat would and should be like.
That is, most ships are somewhat slow and cumbersome, but have a freedom of movement that very elegantly offsets the reduced mobility. IIRC in Homeworld, things happened very fast, as most games try to portray them. I think in reality, gravitational forces and inertia would have profound effects on what you could and could not do with a ship in combat, and this comes across well in Rebellion. It's a much more strategic system, where I think frequent use of Pause is not only reasonable, but to be expected.
The shortcomings were of course the limit of 2 factions, the lack of any sort of randomized map, the lack of any customizable characters, and an AI which we poo-pooed at the time, but while bad, was still better than nearly every game I've played of such scope and magnitude.