They're both owned by Nintendo, so it's totally fair game. The protagonists of the Pokémon series have always lacked that certain flair, with the possible exception of Ash, who had more flair than he knew what to do with. Pikachu had to electrocute him at the end of every episode just to get him to calm down.
Besides, combining the worlds of Pokémon and Mario can only result in good things. The look on Bowser's face when Mario sics his Mewtwo on him would be priceless, and watching Mario try to jam a piranha plant into a Pokéball could provide hours of funny Youtube videos.