The only real issue that I ever had with the BG2 quest bloat of chapter 2 dealt with your travelling companions. Though I like the idea of some quests needing to be accomplished within a certain time frame, I think it was the wrong decision to tie these quests to the first NPCs that you recruit in the Copper Coronet. It is very possible to be balls deep in a side quest when Korgan decides it's time to bail to find his book or whatever, with no chance to make it back to the Graveyard District in time. My wife's first (and only) attempt at the game ended prematurely, having fallen into a similar trap with Anomen - apparently he turns hostile and tries to kill Aerie to boot (not so certain if it can actually happen, though this anecdote is told and retold whenever the game comes up among friends) . The actual amount of quests is fantastic and it makes sense for such a large city.
Compare the start of BG2 to the first quest hub of Dragon Age: Origins, the game that Bioware intended to bring back the IE/BG glory. I feel that we have established the wealth content of Athkatla. Lothering otoh has 2 recruitable NPCs, a handful of opportunities for dialogue skills (persuade or intimidate the Chasind, shopkeeper, etc) and a small quest to utilize each of the possible crafting skils (herbalism, traps and p-p-poison), just to get those out of the way for the rest of the game. Then you kill 3 packs of bandits and roll out.
What I found most damning about Lothering was how bland it felt. The town is your first impression of a town in Dragon Age: Origins, something that usually leaves and impression and sets the tone for the rest of an RPG (like that first time you wandered into Shady Sands, for instance). Athkatla was huge and complex, there were quests everywhere, people running around and even the ambient sounds participated in the fun. Lothering is said to be swarming with refugees, nearly absent of law and order and on the verge of being conquered by Darkspawn - yet the end goal of the zone is to clear those 3 packs of bandits.
I'm not sure where I'm going with this anymore, but TLDR; Athkatla/Act 2 works because it is a big, chaotic city full of meaningful quests where you can choose to do as many or as few as you'd like - many of which with multiple outcomes and even some reactivity from the game world. If you are going to have smaller quest hubs and fewer quests overall, be damn sure that they're meaningful, interwoven and full of c&c.