It's only a matter of time before they get shut down under copyright claim, so I wouldn't invest heavily in them. Especially not monetarily. I contacted Nintendo personally when I was making a Pokemon engine, and they specifically said they don't license third parties to use their content unless they are a registered game company with an established history of big-name game publications. I imagine they don't want another "Mario Is Missing!" in other words, but they take their copyrights seriously. They certainly wouldn't allow it without royalties, which these sites don't pay.

If anyone ever finds one that is licensed, I'd love to hear about it. Not only to see a licensed Pokemon MMO that somehow isn't advertised across the entire planet 24/7, but also to see what game history the company would have. If the MMO is good, it stands to say they may have good taste in past developments.

But again to my knowledge, no company does exist that has a third party Pokemon game license.