Although I do insist that Nathan was unpopular in a lot of circles during the first season.

He was, and if you want proof that despite changes, the attitude can still be encountered, check out the most recent review I got for "Five Lies...", only about a week ago:

http://www.fanfiction.net/r/3570333/

Noah B: see, I liked what they did with him this year - a deliberate greying (and especially that a seemingly straightforward black and white concept, "Noah recruits Mohinder to bring down the Company" instead went "Noah goes off the rails and Mohinder decides the Company is the lesser of two evils", not to mention that instead of ending with Noah victorious, it ends (for now) with Noah re-entering the Company - but didn't like how fandom insisted on seeing him as completely white regardless. And agreed on the separation from the family idea. I'm sometimes fond and sometimes not so much of the webcomics, but I can tell you that the one where they did the split panel image of Noah and Bob having a single face (the phone conversation where Noah calls Bob after having killed the dangerous rogue) and Bob tells Noah that he's still a good Company Man because that's what he is made me feel smug, considering I gave them a similar conversation in "Players".

Next thing you'll tell me there are people who ship Vaughn/Lauren.

*g* I think there there might have been. There definitely were Lauren sympathizers who (rightly) thought she was screwed over, characterisation wise, though they were in a minority.

Sidenote: sadly enough, I thought the best and most dimensional Lauren was written post - "Full Disclosure" was in season 4, when she was a corpse, both in terms of her relationship with Vaughn and her relationship with Sark.