They are usually different enough for me. Ganondorf and Captain Falcon from Super Smash Bros. Melee have more or less identical Specials but I vastly prefer Ganondorf due to his weight, normal moves, and speed. Same with Fox, Falco, and Wolf in Brawl. There is a surprisingly big difference between these three if you with them enough, especially in the Smash attacks. Ken and Ryu were mentioned earlier also, and while initially the same they have changed enough in my opinion. Again, their Special moves are more or less the same (I prefer Ken's Tatsumaki Senpukyaku and Shoryuken), but their regular moves and the combos they can get from them change how even a scrub like me handles them.

I guess I feel people just look at the Special moves and if they are the same they assume the clones play the same, when that's usually not the case.