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Well, for one, it's cool for the people who grew up with pokemon. I'm no genwunner by a long shot, but mewtwo will still always be the coolest legendary. Fuck rayquaza.
Combine that with the fact that he has a realistic chance again due to being a significant pokemon in x/y and a main character in a new movie, and it's not that hard to see where they're coming from.
I grew up with Pokemon and I still love it. I watched the show as a kid, I started collecting and trading cards when they first came out, I've seen all of the movies except the most recent one, pokemon red was my first gbc game, and the list goes on. Hell, I
still play Pokemon TCG (I can't wait for the X and Y set to release in Feb. :P) as well as all of the mainstream handheld games. Pokemon pinball is one of my favorite gbc/gba games, and I don't really even like pinball games...
Again, I'm not saying people
shouldn't want Mewtwo in the next game and I completely understand why everyone loves him so much. I'm just tired of hearing about it all the time. People have been crying over Mewtwo since Brawl came out when his inclusion/exclusion from the game isn't really a big deal. I almost shit my pants when I was a kid and I found out that he was in Melee. When I found out he wasn't going to be in Brawl I said "ok" and moved on with my life. We lost mewtwo, but got a bunch of other interesting characters worth having.
Also no, Rayquaza is by and far the best Pokemon. And no I don't mean best legendary, I just mean best Pokemon straight up :)
How long has it been since there was a viewtiful joe game?
Plus his powers wouldn't really make for a unique moveset...
Relevancy is only a single factor that influences whether or not a character is deemed worthy to be added to the roster. Sakurai has a large pool of characters to pick from, and each has their own reason for why they could be added. Some are popular, some are iconic, some have a good history, some are simply quirky, etc. It doesn't matter how long it's been since there's been a viewtiful joe game, the point remains that he has and unique image that was born on a Nintendo console. Not only that, but his character would fit well within the universe of smash bros and he has a large set of moves and abilities to pull from.
But I think Wonder Red would be pretty awesome as well. I was just saying that Joe's implementation as a character would be more straightforward and obvious, whereas making Wonder Red into a character is definitely possible although it bit more difficult and problematic.