Well, uh... there's a reason fighting games like Super Smash Bros. Brawl only have a roster of a few dozen characters. They don't have the space or capacity for more. Even the latest game systems would not be anywhere close to capable of handling
649 playable characters, each with their own full set of animations, stats, and attacks. It's beyond unfeasible.
This preposterous amount of monsters only works in the main series games because of their simplified nature. The battle system is very straightforward, giving you a few options rather than a full 2D fighter layout. Pokemon have animations, yes, but even in the 3D games they only have about three (idle animation + two attack animations). And the overworld is still basically a grid of square tiles. Etc. The game cartridge has space to hold it and the game system has the capacity to run it with 649 monsters because the core mechanics and layout of the game are so lightweight. On top of this they're able to pile on increasingly more features and mechanics as systems improve. Black and White 2 are full of things to do besides just beating the main storyline (which is lengthy in and of itself), and there are literally hundreds of Pokemon to try out on an ingame team, so I'd hardly argue there's low replay value.
Brawl, however, manages a meager 40 characters - granted with a
lot of extra features and emphasis on graphics, but still. You're basically suggesting a Brawl with hundreds of individual characters. That's just not exactly possible with the kinds of games and systems we have today. To give a little more perspective, the closest thing we have to this right now is the Pokemon Rumble games. Y'know, the ones that look like
[this]. Really basic simplified 3D models with even simpler animations. That's what they can pull off right now.
I could maybe see a 2D fighter Pokemon game as a spinoff, but it'd definitely have to have a narrow handful of playable Pokemon. I also doubt it'd be anywhere near equivalent to Smash Bros. A Pokemon game, especially a spin off, wouldn't have as much money poured into it as a major Nintendo release like that.