It's not a separate game in the single slightest. You're required to own a copy of Super Smash Bros. Brawl in order for it to work, and since its framework is utterly dependent on Brawl, calling it its own separate game is like calling the different game mode mods in Gmod their own separate game. Or Newer Super Mario Bros. a separate game. They're not.
Dota and others may started out as mods, but they're certainly their own dependent game that doesn't require a copy of the original game they're based off of to run properly.
At most, it's its own entity since it does give out significant gameplay/aesthetic changes, but people need to stop lumping Project M as its own separate Smash title alongside the other Smash Bros. games. Otherwise, I may as well say Newer Super Mario Bros. Wii is the best New Super Mario Bros. game.