I can't speak directly for BotE as it's not my area of expertise, but my understanding of it is that - as with Supremacy - it will likely be the absolute last part of the game to be implemented.
Whilst combat is the most exciting part of the game, it is also the most complex - you don't want to program it now only to find that some other essential part of the game interferes with the combat later on. If this were the case, huge parts of the game may need to be changed - or even removed. By programming combat last, you can ensure that this doesn't happen.
There is also the fact that we are still a long way from having a complete model database - or even a working shiplist. Our existing models may also need cleaning up to ensure there aren't any crappy textures or jagged edges ruining our models. Then the shiplist needs an overhaul as we have identified a number of problems with the existing one.
The main part of the combat is the AI though - you want something that will give you a challenge no matter what your skill level is - whilst being true to the individual races. You don't want the Coalition making suicide runs and the Khaorons running from battle, for instance.
Programming AI's is a complex task, but the technologies to do so are improving all the time. The longer we wait, the better the AI will be. I know it's frustrating - you certainly aren't the only one who wants combat NOW - but seriously, the longer we wait, the better combat will be in the long run. BOTF was (From a programming point of view) crappy because it was rushed. It was never even play tested before it hit the shelves. We don't want something similar happening here, right?
_________________"Anyone without a sense of humour is truly at the mercy of the rest of us."