As far as popularity goes Pokémon hands down, but once Nintendo opens up their theme park section in Universal Studio, I think Mario will be everywhere again.

It happened a long time ago.

I dont think it fair comparison, because you include in Mario basically every game that have Mario in its name and that isn't exactly fair because games like 2D/3D Mario, Mario Kart, Mario Party, Mario Sports and Mario RPG are all very different one from another, while Pokemon game are similar, that's basically 5 franchises vs 1.

While true, Mario is much more diverse and all over the place in the video game industry. As Megaoverlord12 and others have stated, Pokemon is a much better multimedia franchise than Mario is at the moment. When was the last time you saw a Mario movie or TV show? Or a Mario trading card game? Or a Mario amusement park, remember Pokepark? Pokemon has seen success in all of those venues and industries that Mario hasn't had in a long time. So I think the comparison is fair.

Depends. Sure, Pokemon is more popular right now and is generating a whole lot more sales. But when we talk about brand recognition, I think Mario has the upper hand. There's just no one who doesn't know who Mario is (in the west anyway). It's a bit like with Disney. Marvel is making serious cash right now, same as Star Wars and whatnot. But Mickey Mouse is still the best-known character they have. If you know what I mean.

I know exactly what you mean. Disney is actually a really good comparison. As great as Star Wars and the MCU are doing, there's just no dethroning that dang mouse!!

I didn't know that happened. If true, then I guess it's Mario by a country mile. 

According to Nintendo:
New Super Mario Bros - 30.80 million
Mario Kart DS - 23.60 million
Pokemon Diamond/Pearl - 17.63 million.
Yeah, DS was the one time where Mario beat Pokemon in handhelds, and it didn't just beat it, it destroyed it!
But other than the DS, Pokemon has reigned supreme on Nintendo handhelds.

Yep, New Super Mario Bros DS & Wii each sold about 30 million compared to 17 million for Diamond/Pearl.

I'd say it's really close. Even in Japan. I mean, Pikachu was chosen as a mascot for the Japanese International football team for the World Cup a couple years back. That's a heck of an honor since you're representing your country of origin. And to think about the Olympics that are coming to Tokyo in 2020, the same year the Nintendo theme park at Universal Japan is presumably going to launch...oh boy. Mario and Pikachu could have a field day!