Along those lines, the Pokemon I've chosen here are more about what I think would be interesting to play, more so than who's popular or likely to make an appearance. Yes, I'm one of those people who like characters in Smash for how they play as opposed to how well they play. Mr Game & Watch? Love him. Lucario? Not so much. So yes, there are Generation 1 Pokemon on this list, but for reasons other than nostalgia.
A great many fighting games have a character that uses the move sets of other characters, like Combot in Tekken or Edge Master in Soul Caliber, but Smash has never gone this route. Yes, Kirby can copy powers, but otherwise he has a pretty solid set of moves that don't change. Ditto could fill this role nicely. You choose Ditto, load the stage and then have a mad scramble to figure out which character you're actually fighting with as your opponent closes in. Yes, he's a fun character rather than a competitive one; am I the only one that cares about Smash being fun anymore?
There are a few reasons behind this choice, one of which is the batshit crazy but still awesome backstory to this Pokemon; "The DNA of a space virus underwent a sudden mutation upon exposure to a laser beam and resulted in Deoxys. The crystalline organ on this Pokémon's chest appears to be its brain." (Pokemon Ruby Pokedex) Add to that Deoxys' awesome and unique design and transformation-based powers and there's something really cool to play with there. Deoxys has four different "Forme[s]", Normal, Defense, Attack and Speed, each with an obvious focus. Smash-wise I'd really like to see a character which has to change between different forms to fight the most effectively, creating a challenging play-style for committed players.
What I'd really like to see as a playable Pokemon in Smash would be a "heavy" character, someone like Donkey Kong, Bowser or King Dedede, who's slower and more powerful. Really, a character like Golem, Venusaur or Kyurem would do just as well, but I have a longtime love for Metagross, the Psychic/Metal type with big stompy feet and a mean face. For me, Metagross was a great Pokemon card when I started playing again at Good Games Blackburn, as I liked Psychic types and he made the deck competitive. For many, Metagross was a "must have" for any team and competition play in the video games. Metagross is tough, strong, hovers a little and has powerful psychic attacks, seems like a fun character to play in Smash and more than unique enough to be a worthwhile addition.
For many, Zoroark was the ideal pick for Smash Wii-U/3DS, until Greeninja took the world by storm. Zoroark is a "Dark" type Pokemon, basically a category invented to make more bad guys for the manga and anime. Zoroark is one of the few dark types to rise above its bland origins to become an interesting character in its own right, with a unique look and plenty of fans thanks to the adorable previous evolution. Zorarok is a tricky brawler, appearing and disappearing, slashing with its claws and stealing items as it goes. In Smash, Zoroark would likely play similar to Greeninja, but with some of the "dirty" techniques that characterise Wario and Bowser, the kind that make you scream out "come on!" as you fall for them for the millionth time.
Ok, hear me out on this one. Pokemon is one of those video game oddities where the fandom is pretty much evenly divided along gender lines, mostly because there's something there for both boys and girls (in traditional marketing terms) when they get hooked as children. For the "boys", there's monsters fighting, for the "girls" there are cute animals to collect (yes, I think the gender division of toys is bullshit, but I'm making a point here and I bought my ex a Fennekin plush for our anniversary one year). Thus, Eevee is one of the most popular non-starter Pokemon in the entire brand's history, being a cute animal with many collectible evolutions, a few of which are pretty decent. A cute little rodent[?] beating down other characters in Smash would be a lot of fun, and maybe there could be an evolution mechanic with the right item? Don't know, sounds fun anyway.
Ok, so I know a lot of people are expecting and/or asking for Decidueye or whatever character out of the latest generation that is currently popular, but this is my list and these are Pokemon I want to play Smash with; deal with it. Unlike most commenters online, I really don't believe that I can know what will be in the game and what the designers are thinking, so these lists are entirely opinion, and unabashedly so. This is for my own amusement, for the most part, so just enjoy it for what it is.
Also, because someone will ask, here is the Metagross card in question: