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They're how the names were trademarked in the Japanese Trademark...whatever (Office?). They're Romanized for your pleasure. I...don't know why (I assume it has to do with the Japanese written language, though). They are NOT the English names, though. At least not until we get some sort of confirmation from NOA/Pokemon USA (I'm sure some will stay, but...most won't).
Ah, well it's simply an accent marker. It's Romanized, not Anglicized.
Trademarked romaji: The official romaji name as given on the trademark filings. This spelling is used internally by Game Freak and is frequently used on official merchandise and other promotional material. Names based on English words often should be read as if they are English words, as opposed to Japanese. For example, Habunake, being the Romaji translation of ハブネーク, should be pronounced "Ha-bu-nake" as opposed to "Ha-bu-na-ke" if it were a Japanese name. Some are just exact transliterations of the name into romaji.
*sigh*... yeah but they don't use Romaji on merchandise, it's ENGLISH