My only issue with ME2's handling of this was simple.
Nu (so sue me, I get a kick out of odd names) spent her time chatting kaiden, and eventually was forced to make the judgement call on vermire. I actually spent nearly 5 miunets trying to puzzle it out. Kaiden died at the end of that, guilt over making a decision that risked everyone outweighing personal feelings. So what happened to harken back to that relationship cut short? Nothing. Having read about the picture (where did the illusive man find it... better not to ask.) and noticing it not being there rather upset me. Sure, it was cut short, but to have it not be there at all was rather disconcerting. Especially given how much of what was done (or not done) in ME 1 carried over. After running into the corprate businesswomen who sends you all across noveria, and whos side quest mess I entierly side stepped, and having that mentioned, it seemed like the logical thing would be the picture there, dead or not.
The Chat with Ashly made sense in context to me, we were comrades, but after all those examples of Cerberus being evil, her whole "How do you know they didn't alter you?" stance makes sense. For a fairly extreme paragon to wind up working for Cerberus would seem like a rather extreme step. Like others I found some of the charicters arguments compelling. I follow paragon a LOT, even when its going to hurt (I am staring stright at a specific gunship right now) but after having his entire team whiped out because of the tratior, and seeing Garrus get so badly hurt himself, I stepped aside and let him have the shot.
I did notice one thing that concerned me, compared to the renegade interrupts, the paragon ones were few (see above gunship example) that said, the ones that were there are brillant peices of work.
I do like what I have seen of the handling of renegade, in ME 1 I had a hard time not seeing such a shepard as a racist thug that cares for no one. The verity in ME2 is much better balenced, sure you can throw the merc out the window, or you can scare the life out of him for info. You can just let the civilans die to secure Zaled's loyalty, or you can point out just how stupid he is acting in the kind of language he understands. Headbut the krogan to get his attention, because thats how it works in their culture. Good writing over all.