Bioware were given a tight 2 year schedule by EA for 3 and sadly it seemed that they just ran out of time. It feels rushed, side quests were no where near as fleshed out as in the previous series plus the ending which was pretty poor by the standards of the trilogy.
The modders have finally ripped the game apart enough to finally start building custom side quests, so hopefully the shallow side quests will be fleshed out over time.