So in the expansions we have only two stories, one per faction. I'm wondering which story is better in i.e. Shadow of Revan, Imperial or Republic? Which story to play first to get the best experience?

I'd say Imperial because it makes more sense. With Republic, you have a Smuggler going up against a freaking ultimate power guy. With Trooper, it makes slightly more sense because they are trained to handle force users, but still...it's Revan.

 

With Empire, you have the Agent which can take out force users alright lore-wise. And then there's the Bounty Hunter which can take out force users easy (BOBA FTW!). Still some issues with Revan being beat by non-force users, but not a huge deal for me.