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I pronounce it as You-No-Vah based on how I pronounce the acronym, USA. Although, now I'm getting used to pronouncing it to how it is said in TV adverts and the Anime.
On the other hand, everyone pronounces everything in their own way based on how they interpret the word themselves so I wouldn't go screaming at someone if they didn't say Unova properly...
I usually pronounce everything wrong, but I'm fairly confident that you-no-va is the way to go with this. It just feels more right than the other pronunciations.