Personally, I love Cath as boss, but I can understand why others have less respect for her leadership skills, after a few less-than-professional decisions over the years. I think she's doing a great job now, but to each his (or, more likely, her) own.
I found
another Greg-as-boss fic, though I'm not sure if this is the one you're thinking of either, Dizzney.
Greg as a Cylon? Oh my. I have to admit that I have been thinking about that for a while... as like the hottest thing ever. Greg as Caprica Six = seduce and destroy. My only complaint is that it involves Gaius Baltar. I'm perfectly fine with slash, but Greg/Gaius just doesn't sound so good to me, mainly because I absolutely abhor Gaius. Still, Greg as a humanoid Cylon would be epic. And imagine the increase in screentime with every version of the identical model
Let's just hope he doesn't get boxed like 3 did.
If only he has shown up in Miscarriage of Justice in the same scene as Cylon #4. Then it could have almost-sort-of been a legit crossover... maybe? I'm not sure if anyone noticed, but the actor who played Cylon #4 (a.k.a. Simon, the one that was playing doctor on Caprica at the 'farm') was in Miscarriage of Justice. And he was wearing basically THE EXACT SAME THING as when we first saw him in BSG -- that is close enough to the same set of scrubs. If Greg had been in the same scene, it would have almost been like him meeting a Cylon.
In general, I'd like to see him in a show that puts more emphasis on character drama and character development just so that we could actually see some more emotion and such.