For some reason, despite knowing Escavalier is pronounced "ess-kavva-leer" I've always said "ess-kuh-vah-lee-ay". I'm not really sure why, I know full well it's the former but the latter is how my tongue instinctively approaches the word. It's the French coming out in me...
The same thing goes for Arceus; I dislike how the proper pronunciation ("arr-kay-uss") sounds, and tend to pronounce it "arr-say-uss" in my head at least because to me that sounds more elegant.
Until the release of Serebii's pronunciation guide a few days ago, I legitimately had no idea how Florges was supposed to be pronounced, so alternated between calling it "florrge", "florr-juss", and "florr-jzz".
Not a Pokemon, but I've also always found the proper pronunciation of Unova ("yoo-noh-va") to be awkward, and so tend to pronounce it "ooh-noh-va" instead.