That's not a good reason though, Sakurai has outright stated the only reason IC are playable was because of their gimmick
To be fair, he has changed his mind before. I don't think he would do it, but don't forget that Zelda and Sheik were founded solely on their ability to transform into each other. That was removed. So their main reasons for being included isn't enough to keep them the same.
Ganondorf's mostly kept the same to have people easily adjust to his new playstyle. He still plays remotely the same in all 4 games, with tweaks here and there. Sure, he lost a lot of speed in Brawl, no doubt, but he also gained new moves and abilities. Also, to be fair, Ganondorf is the epitome of power, and still shows it. The whole point of Ice Climbers is to be a "team" as well, so I can see why he would never entertain the idea of separating the IC's.
Before you compare this to Zelda and Sheik, despite their founding, their playstyles were not actually changed all that much. Zelda is a spellcaster, and Sheik is a ninja. They didn't lose their inherent traits when separated. I didn't like them being separated myself, but they did improve in some ways and got weaker in others.