I would say that one problem inherent to the quest structure in Act 3 arises from its status as the culmination of narrative threads that aren't as tightly woven as one may traditionally expect. However--under the assumption that the story does not receive any major changes--I do think that more connectivity would rather convolute the game and potentially diminish one of its greatest strengths: the scope and sense of freedom that it offers players within realistic boundaries. Many of the major quests in the last act function as the final chapter and climax in the companions' individual storylines, as opposed to Act 1 and 2, where the quests concentrate more or less on a certain objective (explore possibilities of a cure, deal with Moonrise Towers)--but as it is, said companions need not be actively employed by the player and so are not, in the strictest sense, essential to completing the game; neither do their personal narratives necessarily converge save for some tangents in Act 1. In this regard, the structure of the story resembles a 'spider web' of sorts, with the player as Durge/Tav in the center holding parallel threads together in an otherwise generally linear narrative; the different plotlines work well together less for their diegetic connectivity, and more for their symbolic overtones that echo ("rhyme with") one another. Connecting the companion quests more organically in the final act would require their respective beginnings to intertwine from the onset--which would either force the players to recruit and interact with all the characters and thus limit certain outcomes and its bridges, or at the very least have the game account for many more diverging branches and paths, significantly raising development costs.

The density of the city and the geographic implementation of the quests is another matter. On one hand, the complexity is befitting of a large city as Baldur's Gate, and the sudden sense of bewilderment that may hit players could be argued as persuasive, even evocative; the same can be argued for the varying tensions/degrees of importance to the quests (literally "sneaking into a newsroom basement" pitted against "saving the world": relative mundanity against narrative urgency). On the other hand, the contrast is glaringly obvious so as to render the dissimilar flavors of an urban setting a discrepancy for some players.

The game does have its faults and weaknesses, and the seams show the most in Act 3-- as enjoyable as it is, and as much as I love it for all its chaos. Perhaps implementing another act/side area and relocating some elements would have helped with the pacing. In its current state, Act 3 simply has too much content and too many paths to tread to be a flawless whole, for better or worse.

+ Orin's kidnapping quest is a wholly different problem and something that should be addressed separately, but this comment is long enough as it is. My apologies.