Tuthrick: BG2 is very limited in party composition unless you make all characters from scratch. There's no normal thief for the whole game, which is really annoying.
You get Yoshimo, who is a Bounty Hunter, which is a Thief class kit. Although you do lose him later on, you get Imoen back around the same time. Otherwise, yes, most of the available Thief companions are multi-classers, but I didn't find that to be an issue at all. The multi-class thieves are perfectly fine for the main functions you need a thief for (i.e. spotting traps and scouting ahead).
Tuthrick: You also probably can't finish the game without a mage/sorcerer, and other classes feel kind of useless compared to the arcane casters.
This is more of an issue with the unbalanced nature of 2nd edition D&D, as opposed to a limitation of BG2. In 2nd Ed, spellcasters are basically next to useless at low levels and practically overpowered at very high levels. So, for most of BG1, mages might as well be carrying around a bag of popcorn (and make sure they have their will in their pocket), whereas at later levels in BG2, spellcasters are godlike and every combat pretty much turns into a complex, high-level mage duel (which can be a lot of fun, if you like that sort of thing).
Tuthrick: Another thing is that BG2 is filled with too much *epic* stuff and is unfocused, the whole game feels like a huge sidequest-fest. Even the main story is just a side-story to the Bhaalspawn legacy that was only rushed in the expansion. When I see random guards having all +3 equipment, to me that's a signal that something is off.
Not sure what you mean about 'epic stuff'. The higher Epic levels and abilities don't kick in until Throne of Bhaal, otherwise BG2 is just higher levels of the basic 2nd ed D&D game. As far as 'unfocused', again I'm not quite sure what you mean there. There are a lot of side quests in and around Athkatla, but I see that as a good thing that gives a lot of freedom and options to the player. I very much like the fact that in Chapter 2, you are just told to go and raise 20,000 gold, and it is left entirely up to the player to figure out how to do that. You can spend a lot of time in Chapter 2 just doing side quests and the stronghold, as some of the side quests are very substantial. It adds a lot of replay value to the game.
I wouldn't call the main plot a side-story at all. It's a deep, complex, epic plot line that twists and turns and introduces very well the 'legacy' plot in ToB. I'd say it's one of the best plotlines I've played in a CRPG.
Anyway, I don't think there's much point in arguing over which is better over BG1 or 2. I mean, they're in the same series, they are basically the same thing, just that BG2 gives you more of it at a higher level of depth and complexity, for those that want it. BG1 is like the 101, whereas BG2 is the advanced class.