Legacy is HEAVILY based on Armada 2 in more than one way, so it is very very moddable! By far more moddable (is this even a word?) than SFC! (but nowhere near as headache inducing as BC)
Yes the missions were pants, the cloaking button was put on the 'repair' panel and there are numerous other niggles that I have with the game that are classically symptomatic of a game pushed through before it was ready - BUT - when you start digging through the files you see that actually they had planned to have quite different missions, evidently sets for Romulans and Klingons.
I'm afraid guys that there is only one conclusion - the developers had a change in direction and didn't have time to polish (ahem *finish*) the game off properly.
The game as it stands now, sucks, be it as it may - HOWEVER, it's ripe for modding and oh what fun can be had with such a flexible system! I've already ported over CG's Sovereign to my personal game and very easily I have animated bussards and the works - using the same knowledge that I had from 5 years ago modding Armada!
All of the cool stuff from Armada 2 is still in there, we just need to get it working. I don't think that this is Legacy, I think it's Armada 3, with a souped up engine.