I played a lot of the first game, completed the DNA chains, but could not muster the energy for the flags. AC1 singlehandedly broke my will to do collection Achievements. Anymore, unless they're marked on a map like in BULLY or there is an online map of superlative quality, I am so, so done with that kind of crap.
Also could not stand the "therapy" sessions even though I'm fond of that Veronica Mars actress. Talking was fine, but mashing B Button to continue getting chatty during each possible break... and still not getting the completed-every-conversation Achievement was also crappy. But worst of all is the debilitation of the character. You can't strike the doctors - whatever - if I'm locked up against my will, I may want to act out a little. But you can't run or jump or climb, either. You can only walk, and you can't even push past the doctor when he's hanging out in your room. It isn't a "contrast" between playing Altaire vs. the prisoner, it's just broken feeling.
And then the whole "use your Eagle Vision in the clinic" ending was just unintuitive and crappy, too.
Hopefully they work all that out.