MMOs always suffer from these kinds of problems because side-quests arent within the time bubble of the main story, but still lie within the time bubble that they were formed. Yes it seems odd that you can do them out of order, but when you play MMOs you have to play them with that thought in the back of your mind that "this quest came out in 2.0 so I gotta treat it like I did it in 2.0 when it made the most sense."

Just can't be helped since MMOs are dynamic while single-player games are static.