I don't think it's fair to say that pokemon should be male/female based solely on the name. Think about it, there's such a thing as a king cobra, but that's just it's widely used name, while it has a scientific name that has nothing to do with being male or female. If the Pokeworld is anything like our own, Mr. Mime, Geodude etc would just be common, or even area specific names.
It's a little hazzy though when the anime is taken into consideration as the pokemon usually say their own name, but others such as Onix and Charizard just growl....and both Krabby and Kingler would be named "Cookie" :P
So all in all, the physical features really determine what the pokemon appears as, but like SwiftSign already said, the animal kingdom is full of colorful males and more rugged looking females, which all in all, make this topic fairly useless.
If anything, those Pokemon that are only either male or female need to have a polar opposite, otherwise the species will die out. Also, most of the genderless Pokemon most likely DO have genders, such as many of the legendaries, like the birds. We just have no idea how they mate, when mate, or the conditions required for their offspring. The anime confirms this with the baby Lugia, and pokemon snap has Zapados(I believe. could be one of the other two) hatching from eggs.
The only pokemon I think should truly be genderless is the PokeGod, the lake guardians, the god dragons, and mewtwo. The gods etc because they are all suppose to be one of a kind, and Mewtwo because I like to think the scientists were smart enough to not give that thing a chance to breed.
