"I've seen lots of questions in the Story Questions Thread about the possibility of Armada troops or even the Elites joining the PC as Companions. When I see player posts speculating about what the future plot holds (always a fun pastime), these grants are assumed - Rooke will join us after betraying Kane, or Kane will be granted after El Dorado.
I'm here to tell you, I don't like the idea - the way I'm looking at things right now, I don't see it happening (at least for a looooooooooong time). I'll tell you why:
There many different types of villains out there: the bumbling bully (Popeye's Bluto), the nemesis (he's just like you but evil: think Belloq to Indy Jones), the evil genius (Hannibal lector and so many more). One of my favorites is the Force of Nature - monolithic, unstoppable, and unfathomable: you're scared of them because you can't empathize with them. The shark from Jaws is the most extreme example of this, but another one that I dearly love is the Borg (pre Hugh and I, Borg: the season 2 and 3 Borg). That's really what I was aiming for with the Armada.
They're tougher than you, they are relentless, you have almost no window on their thought process, and they don't care what you think. We're deliberately trying to keep them as "other" as possible, to emphasize their creepiness and maximize their potential as enemies.
To give a re-programmed Armada clockwork as a companion would take some of that mystique away. The worst thing they ever did to the Borg was to give them an empathetic identity, and then a queen. I want the Armada to be nothing but an enemy.
A disclaimer: if a really cool idea strikes me later on, I could change my mind. But for the foreseeable future at least, I don't like it. No sir, I don't like it at all."