First off, the "Ray" part... considering there's a "ray" in the English language, people probably associated it with that the moment they first saw the name, but given the English language and its tendency to vary the pronunciation of vowels without so much as a hint, if I said it could be pronounced "Reh" instead of "Rey", that probably wouldn't be too hard to swallow, would it? So, skipping the ッ half-sized "tsu" (a little beat sound used in Japan, commonly represented in romanization through a double consonant, which I doubt several westerners are even aware exists), let's move onto the "Quaza", which is where the main difference between the Japanese and western pronunciations stem.
When most people see a "qu", it's probably a given for them to pronounce it as "kw". However, what they fail to realize is that there are several exceptions to this rule, especially in other cultures. In particular, I've noticed that in Aztec names, they tend to be spelled with a "qu", but are pronounced as just your typical "K" sound. Rayquaza's design itself looks like it might've taken a few cues from Aztec mythology (particularly the famous Quetzalcoatl), so I wouldn't be surprised if this is precisely what they were going for. The following "a" being pronounced as "uu" in Japan still kinda baffles me, but an intention of an "uh" pronunciation might work, albeit stretching it.
So in short, I think Rayquaza was really intended to be pronounced as "Reh-kuh-zah" by Pokemon's western audience. If anybody would like to add their thoughts on the matter, feel free to do so.