I voted Docter Mario. Unlike all other clones, Docter Mario is Mario, unlike all other clones, who aren't the same person of who they're clones of. And Docter Mario is also much more simular to Mario than any other clone. Ganondorf is much heavier and slower and much more powerfull than Captain Falcon. He also lacks the triple A attack and the Knee of Justice.
Pichu is much smaller than Pikachu and hurts himself when he uses an electric attack.
Falco is much faster than Fox, he jumps higher and is heavier. His Reflector also sends people upwards instead of spiking them.
Roy is slower and more powerfull than Marth. He also is lighter, has a shorter sword and his sweet spot is in the center of his sword, where Marth's sweet spot is at his tip.
Luigi is far to different from Mario to be compared. Just three of his B attacks are the same, all else is totally different for the two.
Docter Mario is a bit more heavy and his pills have a different course than Mario's Fireballs. Too little difference IMO.
Capt. Falcon was a bounty hunter before he was a racer. Therefore he is very suited for a fighting game.
Ice Climbers are about the only unique characters in the game. They were the reasons everybody started hoping for Plusle&Minun, Mario Bros. and Baby Mario/Baby Luigi characters. They are far from weak. Their smash attack also sends people far, is there are two people attacking instead of one. It is also very fun to play Coin Match with four Ice Climbers. And they also give one of the hardest challenges in the game.
Pichu is perfect for experienced persons to battle less experienced persons.
Just like Ice Climbers, Mr. Game and Watch is unique. All his special attacks are unique. His loggy play is also more unique than anything else. Besides, he was the first character Nintendo ever had. Removing him would be like destroying a Greek Temple to build a cinema in its place.
I think that no clones (except for Dr. Mario) should be removed, but just changed.
Link should use the weapons he used in MA, WW, MM, OoA and OoS, like the Gust Jar, Roc's Cape, Magnetic Gloves, Deku Leaf, Deku/Goron/Zora/Fierce Diety Mask and perhaps even the Four Sword.
Falco should use that big, big gun he uses on that picture of him that was also on the fake cover of SSBR.
Pikachu should use Volt Tackle, Thunderbolt and Pichu should use Surf and Thunder Wave.
Dr. Mario should be made a different colour for Mario,
Luigi is different enough already.
Roy should be replaced with Eliwood (Eliwood has a large role in FE6 and was the main character in FE7, while Roy only appeared in FE6 and had a very, very, very minor mention in FE7. FE6 was also never released in the western world). Other than that I think that are good enough as they are.
Ganondorf should use his magic or his swords. I really want to meet the people who made Ganondorf for SSBM, just so I can yell at them. What were they thinking to make a him a slow, heavy physical character when in OoT he floats around like he is weightless and he always uses magic to attack and in WW he jumps around like a ninja grasshopper and uses his two ninja swords to attack. What have they been smoking when creating him? That stuff must be good.