You know, people give Mass Effect a lot of crap for its side quests (and that's understandable), but I really enjoyed them and played every one I found. I really just enjoyed all the little bits of backstory the side quests had, I really like the Mass Effect Universe.
That said, for ME2, besides fixing the obvious flaws with the side quests that I won't mention because they've been discussed to death, I think they need to make the side quests make more sense within the main storyline. What I mean is, it didn't really make sense in ME1 how I was in a race against time chasing a rogue spectre across the galaxy with the fate of all sentient beings at stake, but then I'd take a break from that to travel to the opposite side of the galaxy to help some random nobody track down his brother who he hasn't heard from in a week.