Bane/Joker were also the only villain combo we actually saw interact. Scarecrow and Knight talk like twice over the radio with each other, and never actually operate in the same space, despite such an image in the trailer.
But the biggest thing Bane and Joker have going for them in AO is that they were both developed, both hyped as huge threats, and importantly neither of them were thrown under the bus to hype up the other. Rocksteady I've noticed has a habit of doing such a thing with their villains in order to establish how big a threat a villain is, the classic examples being Bane in Asylum and Strange in City even more so.
In contrast look at the hotel scenes in Origins - they're a masterclass of developing villains with conflicting goals and establishing power dynamics. Joker is shown to be wild, unpredictable and brilliant, and Bane is shown as tough, pragmatic, resourceful and not scared of the Joker. They are two villains who dislike one another (more so from Bane's direction) but also share an uneasy alliance that is quite satisfactorily never quite broken. Bane develops a good enough knowledge of the Joker that he knows that even after trying to kill each other on the hotel rooftop, that the alliance is easily reforged with the right idea (the heart monitor gambit). His men easily slaughter Joker's, and he's the one that discovers Batman's identity, trashes the batcave, and wounds Alfred, but simultaneously it is Joker that sets everything in motion.
Much, much better than "He was your puppet Ra's!" or whatever the hell the Scarecrow/Knight alliance was meant to be. Seriously, someone at some point had to realise that Knight was a terrifically boring character, but God knows someone else must've had a terrific ***** for the guy, given that he swallows up so much of the narrative compared to Scarecrow.
You guys said it all.
