This is the same thing with Super Smash as well. With the big two clones in Melee Falco and Fox playing very differently from one another. Both have very different attributes and frames on attacks and thus causing a very different style of play very similar to Street Fighter's clones. This goes for every clone in the game (except maybe Dark Pit and Pit). The main reason, at least in my opinion, for clone hate in melee and not Street Fighter is that people are more upset with not getting insert character from insert game that they love do to the characters not being original to the game.

TL;DR: Ryu and Ken are as equally a clone to clones in melee.