Well it all goes back to the puns in the names.
Let's see:
Rayquaza. I've pronounced it ray-KWA-zuh, but after hearing it pronounced ray-KWAY-zuh in the movie, I think I'll switch because it's Ray as in beams and stuff, and Qua as in quasars (something that has to do with science, I think--and you pronounce that "Qua" as you would the word "way"). With that in mind, quasar's syllable should be the right fit, regardless of spelling, since it is a pun. Which would have to sound right, but not be necessarily spelled right.
Deoxys. We all know it's a shortened for of DNA's full form. With that in mind, it should be pronounced dee-OX-ees, since in deoxyri... you get the "I" sound and not a hiss sound. But I like to go with whatever the animé says, like with *moan* Illumise--ee-loom-EE-zay. And in this case, I have gotten used to dee-OX-sis.
And with Sceptile, all I have to do is ask: how do you pronounce Scepter?