The real reason is simple. The Virtual Console runs original code, the XBLA games are ports that are programmed to run on the Xbox 360 and often have to be done entirely from scratch due to the lack of original source code.
If you're developer X and want to release your classic NES game (For one example) on a platform, you have to do no programming to bring it to the Virtual Console. It's just going to be the original code that was on the rom chip in the cartridge back in the day running through Nintendo's Virtual Console NES emulator that recreates the functions of the NES hardware on the Wii.
If you want it to be an XBLA game, the publisher has to actually do some work, typically by programming a game for the Xbox 360 that replicates the original.
Few XBLA games (One exception are the Sega Genesis releases from Sega that are running original code through an emulator that Sega commissioned Digital Eclipse to program) are original code. Typically, they're like the Namco, Konami, and Midway XBLA releases. They're fresh ports that are natively running on the Xbox 360 rather then original code running through an emulator that replicates the functions of the original arcade hardware. That's why for example the popular patterns from the arcade release of Pac-Man don't successfully work with the XBLA release. It's not the original code being ran, rather, it's fresh programming designed to try to replicate the arcade original.
Microsoft doesn't have an emulator to run NES code available to potential publishers. So if a publisher wants to bring a specific NES game to XBLA from their backcatalog, it's typically easier and more economical to program a version of the game from scratch then it is to go to the expense of programming an emulator for 1 game.
In short, it's much more expensive to bring a classic game to XBLA then it is to the Virtual Console since Nintendo has done all the work to program a range of emulators. That's where this new Game Room comes in with the Game Room development team creating a range of emulators for various classic consoles and arcade hardware. Much like the Virtual Console, a potential publisher just has to submit the original code to be released. No programming expenditure happens since a company like Konami isn't touching the original code to a game like Time Pilot in Game Room.
The only cost a Virtual Console publisher encounters are to pay the ESRB to rate a game and Nintendo's publishing fees since they're essentially recycling past programming work. It's much more expensive to bring a classic game to XBLA since you actually have to have a team of programmers working on it on top of the similar fees a VC publisher has to pay.