The way you pronounce the names really doesn't matter. There is no rule of thumb for the proper way to say them as they are not proper English Words. A common one would be Nidoqueen (you could take the "i" as long and pronounce it "nidoqueen" or see it differently and see "Needoqueen" It's all matter of preference. the anime is not a solid foundation as to the names since people are just reading from a script, and many probably probably are in the situation of how to pronounce it, it's not a very big deal to them.
Hmm, maybe... although I don't really know the proper pronunciations, I just guess.
I saw one of the anime episodes a little while back and didn't realize that Gliscor is pronounced "Gliy-score" and not "Gliss-core".
