If Missingno. were to be a Pokemon, it should be a Glitch Pokemon, like in the game. I say yes, but as long as they don't change the type and appearance.
Don't give it a stupid type like dark/ghost as so many people would suggest. Give it Normal/Bird (I'm being serious about that).
I want to take place in a game that is almost the same as the canon games, but make it a non-canon spin-off that breaks the 4th wall by making some people acknowledge the Missingno. An evil team will appear that goes into Glitch City and you follow them, fighting a powerful Missingno. at the end. You cannot catch it though, and you'll have to preform some mad thing like the Old Man Glitch or something.
HOWEVER. As in Red and Blue, having the only Pokemon(?) that can level all the way to 255 will come with risk. I.e. it can erase your save without a moments notice and not as a glitch but as a feature.