Best,
-Characters, story and excellent writing/universe, best atmosphere I've ever experienced in a game (even surpassing my long time favourite Mafia), I also love how I've really grown fond of some of the characters, for instance Joker, made me laugh out loud multiple times. Characters like Jack which I had doubts about, ended up pleasantly surprising me too (although there's plenty of ppl who disagree with me).
Biotic combat is a lot more fun, had more fun playing Sentinel this time (instead of just choosing assault rifle bonus like in ME 1 and just use that most of the time), the universal cool down makes more sense and it's fast enough to still have nice combat.
Worst
Heat sinks, I can see how the combat was made a bit more intense with it, and I applaud Bioware for the courage to try and change something this essential in the game (and the Mass Effect universe), but it still doesn't make any sense. Two years ago not even the best tech and weaponry would use it, but now it's the ultimate standard, and every civilization/party uses them? Inconceivable! Kinda disappointed with it, I really like the technological explanation to not needing ammo in the first game, they kinda negated it now, hope they'll take it back in ME 3, but probably a fat chance.
The 'dumbing down', not enough different weapons (and always an obvious best outside of the heavy ones, no real choices), I miss some of the skill bars, stuff like that (but I'm kinda of an 'classic' RPG nerd, so that explains it), this also includes the mission complete screen (would've preferred the ME 1 way and report back to TIM through the brand new com room, they installed it for a reason, and it would've given players the choice to report or not). The armor is an upgrade though, seeing how you can change parts of it (but it still needs more options and more balancing, the death mask not giving any health or damage reduction bonus is just weird...), although your squad lost all choices, makes them have more of an own personality, would've preferred to have more choices (which mattered) again, but I guess we'll have to deal with it.
(also didn't like how the areas became significantly smaller, no presidium style areas in the game, everything was small corridors and small plaza's connected, I'm sure this is due to the console hardware restrictions though, so I guess it can't be helped, too bad for us pc users, but hey, better this than nothing)
It's a weird game, when playing, I got annoyed at some things, but ended up forgetting all the annoyances while in awesome combat or during brilliant conversations/cutscenes. I miss a few things and dislike a few others, but all in all, I'll have to say I like the game even better than Mass Effect 1 (and that's hard enough).