1. Anime canon Mewtwo
2. Slowking
-This fucker is without a doubt the most intelligent non-legendary Pokemon in existence
3. Alakazam
-High IQ, but scientifically IQ means beans so who knows?
4. Gardevoir
-Shown to be able to talk via telepathy so I'm assuming high intelligence
5. Lucario
-Same thing as above
6. Lugia(?)
-It can talk clear as day, shows logical reasoning, and is sapient, but only in one movie, but then the same could be applied to Lucario and Gardevoir so who knows?