A lot of 'em are likely to be clones. But probably clones with different type advantages and weaknesses. And as far as implementing type matchups, it can be done with a bit extra damage % being done rather than going bonkers and do a full double or quadruple the damage. So that it becomes possible for an Aggron to hold its own against a Blaziken, but it's gonna rack up damage faster than it would fighting something else, and maybe be more vulnerable to flinching to certain attacks.
A lot of attacks would probably translate over pretty well. Most priority attacks would probably work like pikachu's currently existing quick attack or Ike's quickdraw- a speedy dashing attack that is more often used to close gaps than anything else. Sucker Punch and Counter would obviously work more or less the same as Marth's or Lucario's. Fliers will probably 'float' at normal character torso level and have many jumps (ala kirby, pit, jigglypuff) to gain altitude and initiate swooping and dive bombing attacks. Projectile moves can be done quite easily and have potential to work in different ways and directions, as exampled by ivysaur's razor leaf and bullet seed.
I'd imagine that there would also be some pokemon you wouldn't be able to play as due to size/power constraints, but would probably work well as bosses. We've already fought Rayquaza in Brawl, and Onix is a pretty big, serpentine pokemon that would probably be better as ai controlled boss fight than a playable character that would have crazy reach advantage.
One of the more interesting things would be variable movesets for each pokemon, giving each person their own fighting style even if they're using the same pokemon. For example, Blaziken could potentially use both high jump kick and blaze kick, or just use one and augment type and attack styles with fire punch or brick break.
Variety... you could easily have an infernape and blaziken with the same moveset, but they would still feel different because their heights, their jump, their speed, their hitbox wouldn't be the same. Hell, even the same move might have a different execution based on the pokemon using it. Think of Mario's fireballs vs Luigi's.
I can even see leveling up pokemon and assigning neutral EV points to stats to customize a character. SpD and Def to decrease damage taken, HP to reduce knockback at higher damage, and Atk/Spc Atk to boost the effectiveness of moves you like using.
Plenty of moves that can serve as default 3rd jumps, Up+B. Sky uppercut, Bounce, Waterfall, Fly, Flare Blitz (basically, Fox's up+, etc.
It would add depth and extended playability to the game if you have to fight to level up and unlock new moves/pokemon to use. I've always likened it to unlocking weapons for characters in SC.