I'm not as creative as Sakurai is, so I wouldn't've thought of things like ZSS or PT. However, here are some characters I would've liked to see:
Koopa, Rayman/Megaman, Swampert, Heracross (to represent all four generations of pokemon), Roy with a fixed moveset, Toon Link less clonish, Falco less clonish, Animal Crossing boy, Taboo, Isaac
Bosses:
Bowser Jr., Dr. Robotnik, Herd of Pokemon, MGS Boss, G&W boss (a black 2D figure that copies your moves, like the opponents you'd have in the G&W games), LoZ character that I don't know,
Assist Trophies:
Globox/Phoenix Wright, K. Rool, Chunky/Lanky, E. Gadd, Midna, Wolf Link, IC Pterodactyl, Tom Nook, Knuckles, Tails, Pelipper pokeball, Wailord pokeball, Football enemies from SMW
Stages:
SSB Saffron City, SSB Hyrule Temple, Bowser's Castle, SSBM Mute City, SSBM Flat Zone, Bigger Final Destination
Misc.:
Voice acting in SSE, Plot fix (I hear it has problems), More stages, More FIGHTING music (the soundtrack is good, but hardly any of it is motivating me to kill my opponent), More ACs that actually represent something (Dr. Mario, Shadow/Silver the Hedgehog, AND FOR THE LOVE OF JEEBITUS SHINY POKEMON), 100/75 single player event matches, customizable difficulty on event matches, TOXICROAK trophy,
I probably wouldn't actually implement these, but they would be things that would definitely have been nice to see (assuming they worked out alright).