Someone on my Twitter feed speculated something I find likely about the A & B scenarios: Capcom was very open in interviews near the start of the game's development that there wouldn't be separate Claire & Leon scenarios. There would be one campaign featuring all the characters, and that would be it.
Somewhere along the way, the devs changed their minds and went back to the original A-B system. However, by that point, it was too late to make unique scenarios for both characters & link the campaigns together properly.
Considering how the 2 campaigns only kinda-sorta link together in odd & un-emphasized ways and make no logical narrative sense together, I find that explanation very likely.
Unrelated to that, though, there's kind of 2 plot holes in the remake related to Mr. X that's really strange considering they WERE addressed in the original game and they both involve objects falling from the sky: in the original version of RE2, you witness the helicopter crash in the B Scenario. You see a police officer calling a helicopter down, but he gets jumped by zombies & accidentally shoots the helicopter pilot, causing the crash. In the remake, this never gets explained. The Helicopter just crashes for no apparent reason.
Likewise, the original game also shows Mr. X's arrival in the B scenario: there's an Umbrella helicopter that's carrying a series of cylinders containing Mr. Xs. It drops one into the police station, and there he is. If you play RE3, you can even find the corpses of the OTHER Mr. Xs that Helicopter was carrying in the city. However, in the remake, he just shows up. He has no introduction whatsoever.
Those 2 scenes missing, to me, is more indicative of budget cuts then anything else.