If you think about it, very few pokemon actually have a visual indication of special attack capability. Sceptile, Togekiss, Gengar, PorygonZ,... the list goes on and on. For most special attackers, the attacks just kind of "come out". If you've played any of the 3D games, that's exactly how most of the special attacking pokemon attack animations look. A beam just kind of emanates from their bodies or their hand-like appendages, if applicable.
In general, I think we should pick a pokemon design that looks good, fun, and interesting. As for visual support of physical or special attacks, it's not a big deal. Dugtrio gets Sucker Punch -- tell me how the hell THAT happens, considering it has no arms?!? Lots and lots of pokemon have moves that don't fit their visual. If we try to design a pokemon visual that supports all the moves and abilities of the pokemon, we might up with a bizarre "swiss army knife" design.
Don't get me wrong, there are some very good multi-functional designs posted. (CyzirVisheen's comes to mind as a good example) But, I hope people don't put too much focus on that part of the design evaluation.