Well Origins is a weird case in that it really has no right to exist. It really was just a game made to make money for WB off the Arkham name because Arkham Knight was taking so long to develop (there was a 2 year gap between Asylum/City and then Origins, while there was a 4 year gap between City and Knight.) WB wanted another game but Rocksteady was too busy so they had WB Montreal put together a game based off the engine Rocksteady had. And to be fair, it wasn't that BAD of a game overall. I played it for a little while when it came out but at the same time, WB, to promote the game put out Asylum and City in a Humble Bundle and I got to play Asylum again on PC, and playing it again on PC reminded me how much I loved the game and I decided to just send Origins back to Gamefly and play Asylum again. It wasn't until the Arkham Knight fiasco and WB gave everyone who got it on PC every other Arkham game, so I had a free copy for PC that I decided to go back and play it again. And while it was definitely my least favorite of the Arkham games, I still had quite a bit of fun with it.
Problem is that the game REEKED of "quick cash in." It was called "Origins" which would imply that it took place before Arkham Asylum, yet everyone was using modern technology that was later than Asylum (4 years later). In addition, it took place before Asylum but it introduced separate advanced gameplay elements, which didn't make sense to introduce in a game that took place before the others because there was no logical reason as to why they would be taken out. There was really NOTHING from a story perspective to link it to the other Arkham games other than it had "Arkham" in the title and it introduced the Joker. It didn't feature the same voice actors as the other Arkham games. It's supposed to take place in the entire city of Gotham, but the map was smaller than that of Arkham City, which was supposed to be a SECTION of Gotham. It pretty much just featured C-List Batman villains that you'd have to look up more often than not. It had a COMPLETELY unnecessary and unwanted multiplayer mode that was loved about as much as the multiplayer in Bioshock 2. In addition, it was by far the most buggy Arkham game, and WB didn't even fix all the bugs because (
and they said this publicly) they wanted to focus on money making DLC as opposed to fixing the damn game. As much as I complained about how unoptomized and shoddy the PC version of Arkham Knight was, I don't think I could count the bugs I experienced on half a hand. Conversely, on Arkham Origins (which I played AFTER Arkham Knight meaning it should have been more stable) I encountered numerous bugs, one that prevented me from beating a boss numerous times because they would be teleported out of the area for some reason, and another time when I almost lost my data because the game crashed at a save point. And finally, it was the least enjoyed Batman game by a significant margin (we're not counting the Arkham Knight PC score because that's based on port quality as opposed to game quality.)
It seems to me that basically WB and Rocksteady don't want people to associate Origins with Asylum, City and Knight, as it A: Is not really in the same canon, and B: Wasn't made to the same high standards as the other games. If it were up to me I'd just include Origins if for no other reason than to make the Remastered package more appealing (3 games sells better than 2) but given Origin's undeniable reputation as the "black sheep" of the Arkham games and separate standard they set with it, I sort of understand why they haven't included it in the Remastered package.