is there ever a reason I would want my 2 recruits to be from different factions? Having them both be the same seems like a huge benefit. sure if i have a hidden recruit in a faction that my opponent is showing I am secretly benefiting, but why wouldn't I just consolidate my effort on 1 faction?
Well in this issue you have several points to consider, of course seems as best to have both recruits from the same faction, however you could have the bad luck of choosing a faction that other users use a lot to get resources, this would mean lots of high numbers making it very hard for you to advance the allegiance track. it's a "all the eggs in the same basket" kind-of situation
The tier benefits from the allegiance track only benefit peope with a face up recruit of that faction. correct? In my game, purple had a face Icarite who gave 1 extra Bliss when purple placed a worker alone in the Cloud mine. Once the allegiance track benefit added another +1, this meant that purple could gather 3 bliss from 1 placement. Green's recruit benefit in no way was as strong (especially in a 2 player game). Is this normal?
Yes, if the dice in the cloud mine sum 9 or more, the second dice, from purple on this example, would gather the 2 standard clouds +1 for the Icarite recruit, however he would suffer the knowledge increase.
Finally, why would I ever take a recruit rather than the star from the ethical dilemma? Free star seems like such a no brainer to me. I suppose you could hope to draw a recruit that you could immediately put a star on if the allegiance track is complete so you get a star and a benefit but that is hardly a guarantee. what am I missing here?
Well, this is a matter of strategy, if you are focusing on a single faction not only you would get the same star at the moment of reaching the "face-up" point in the allegiance track but would have an additional ability from that recruit, so seems to be a good bonus.
This are all choices to be made to have a better strategy in the game and to know that each player can play the game in a very different way and have a different experience.