Rocketman, just in terms of overall gameplay, I think City is the best because the combat and everything is so smooth.
But there are certainly things I like better about Origins. I like gadgets like the remote claw the best, it's my favorite gadget ever in this franchise. I like the Batcave and also that you can do the challenge maps or training maps during the game and you can improve your overall stats through the maps as you play the campaign.
The challenge maps are also a TAD easier which could be good or bad depending on how you feel.
But I really think the boss fights in this game were fantastically constructed and a great advancement of Arkham City.
Also while I think City had the best overall controls and combat, I think Origins had better hit detection for double counter moves and hits. Frequently in City, my Batman would start a double counter move and only grab one enemy while not being close enough to grab the other thug who still gets a hit in and breaks up my combo.