I do exactly the same thing with my texturepack (based on the 32x Gerudoku pack).
But thats one of the things I love about MC. Default MC is really ugly as hell. But with the right texture, it really can become a thing of beauty. And its so darn easy.
Heck just last night I borrowed the skeleton and spider texture from an entirely different set. Now skeletons are wearing battered old armor, and spiders look like giant jumping spiders.
Update: As an experiment I replaced the ugly old cobble texture with an embossed block. I think it looks rather nice. How about you?