Part of it is, of course, Game Freak logic, though my theory is that by the time Black and White were released, they'd already planned and started working on the sequels, and decided to set up BW2 with BW. In Black, you catch Reshiram, and N catches Zekrom, while two years later, in Black 2, N rides in on that same Zekrom he caught 2 years prior, as Reshiram had been caught by Hilbert/Hilda (Gosh those default names are weird), and Nate/Rosa catches that Zekrom later on. Point is, these are not a third game, but an actual sequel, and thus Game Freak made it so it'd all make sense when you look at both sets.