There's a pretty easy way to make these still rewarding. Not to pull from WoW but a zone reputation system would be nice, make it have small benefits like faster ground speed to catch up during the MSQ or more bicolor gemstones per fate etc. Small enough that they aren't required but are a nice benefit to those who want to complete them.

I think from what I remember they nerfed the exp and put it into the MSQ so people wouldn't feel required to do the side quests, so they likely won't do that unless they become available after the MSQ is complete.