I think most of us agree that the faction quest lines are far and away some of the best parts of the game. However, I'm pretty disappointed with the lack of any real consequence from the decisions you make in them. Of course it isn't going to be Baldur's Gate level of variety, but I just redid the Crimson Fleet one during one of my NG+ jaunts, and this time I chose CF instead of UC. I expected there to be some repercussions back on Jameson, since, you know, I just helped annihilate a huge fleet. Nope, nobody gives a fuck that I just landed my ship at the spaceport, walked through the scanner, continued my other quest with the UC guy that sent me on the CF one in the first place, etc. I was expecting to have to shoot my way to the Lodge or something. Nope. Not even a bounty, which I've gotten for accidentally hitting a fucking UC ship when trying to help them fight pirates. Blow up their whole fleet though? Nah, no bounty.
The only real downside to selecting the CF seems to be that now I can't do the UC mission board. Boo hoo. I can do the CF missions if I care (I never do any for anyone), and now all the cool people I met during the quest are still alive instead of me feeling vaguely shitty for murdering them if I chose UC. (And I didn't even kill the two UC people you get to know, since I persuaded them to give up.) And now I can go back to the Key whenever I want and put those 2 unique items on any ship I want in the future. Oh, well it could be considered a downside that now all CF ships are friendly, if you really like killing them for some reason. Still plenty of Va'ruun and Ecliptic to kill though.
I get why they didn't make it so that Jameson is completely hostile, because that would require reworking tons and tons of quests if you decided to do the CF one first, basically doubling their workload, but it is a pretty big letdown to see just how little it mattered. Andreja "loved" it when I chose UC, but didn't give any reaction, positive or negative, when I chose CF. I know other companions think differently, but at worst you just dismiss them before making the final jump and now it matters even less. When I finally settle down for my post-NG+10 life, and ever get back around to doing that quest, I see no reason not to choose CF again. Unless someone can remember a benefit I'm forgetting for choosing UC?