Origins does have the best story, but it's easily the worst game of the three potential candidates for the collection (it's far better than Knight, IMO). The combat is completely broken until you get the electric gauntlets, and it's no wonder Rocksteady doesn't want it paired up with its own games.
I'm shocked (lol) people like Origins this much. I had a very hard time shifting to the stuttery nature of the Origins combat flow from the buttery smoothness of Asylum and City. Maybe if you're not constantly going for perfect fights and triple digit combos it's not as big an issue, but it was a constant frustration until the gauntlets, which ironically just make the combat flow almost identical to the Rocksteady games.
I won't miss it, and I don't really think it belongs in a Rocksteady collection.