Rotom Pokedex scanned all the Kanto Pokemon, even Mewtwo and Legendary Bird Trio, but it didn't catch a Mew. Mew is a rare Pokemon to encounter, that's why it couldn't see it nor scan it. Also, this was Mew's first physical anime debut in the main series besides those dream or fantasy...
Now I understand why everyone is disappointed about Ash's some mons, Croagunk, Rotom, Tracey being absent, but it's not their fault they rushed it, this show only runs for 22 minutes and they didn't have time to put them all of them in one episode. There's no way to expend it to have more time...
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