And to answer your question - there isn't really a reason, I just more or less didn't think of it. I know little about the Jihad, let alone RotS era, so it doesn't really jump to mind. No reason we couldn't run one there, but from the looks of the vote, it wouldn't have won the race anyways. If I put it up there and people start screaming for the ability to change their votes, I'm more than happy to start then.
As for who would run it...I guess that depends...from what some people have told me, its basiclly the uberpower of the universe at that point, and I'd be a little uneasy letting someone run it. What would likely be done is what Dave B did with the TH in 62 before the time-jumps: let the players all play people who sit on the ruling council(that would be the Paladins, correct?) while the GMs control the Exarch, and just keep the faction running very close to whatever the players decided(unless it seemed to run counter to the good of the game, or it seemed like someone was trying to game the system). But thats just an initial thought at this point, I'm not really worried about it unless people want to run it then.
Damn...means I need to buy some new books. Crunch, can you tell me which E-Books I'd need to buy to get the necessary military and industrial information to setup the game, please?