Part of the problem is Larian giving *everything* (except Minthara, prior to the recent patch) to the "good route" even when it doesn't make sense.
Think about how much different the balance of content in Act 2 would be if saving the Grove locked players out of infiltrating Moonrise Tower. That's three vendors, a large amount of conversations and backstory, and the experience of working undercover and receiving quests from Moonrise characters.
Another part of the problem is Larian deliberately punishing "evil" choices - sometimes in nonsensical ways.
Shar commands the player party to kill Ketheric - she despises him for his betrayal and use of the Shadow Curse for his own ends. But killing Nightsong for Shar and breaking Ketheric's link to the Shadow Curse results in the immediate deaths of everyone at Last Light Inn... despite them being Ketheric's enemies. What if Shar had seized control of the shadows and commanded them to swarm Moonrise Tower instead, sensibly supporting the party's assault? That could've been a fantastic cutscene, and it would offer a significant benefit to the choice.
Much has been suggested (here and elsewhere) about alternate companions, but even simple thematic exclusives could have helped balance the routes without heavy investment of development resources - if Larian cared to do it.
For example, offering Lump and the ogres a feast of tiefling flesh could gain their allegiance as camp followers and allow unlimited use of Lump's War Horn for the rest of the game.
