This is is a really tough question. I mean, they are both nerdy in their own way. It's like...trying to compare apples to...pears. They are both similar, steams and coming off trees and often green or yellow, and have a similar texture and all, but they aren't exactly the same thing.
...that became very convoluted rather quickly...
Anyway, I voted Yu-Gi-Oh! for the express reason of that everyone in the show itself is a nerd. I mean, let's face it, everyone plays card games and nothing else. It's like...if Magic the Gathering had completely taken over the world and the world revolved around that single activity.
Yes, in Pokemon, they go around training, but that's the thing. Each person can do what they like with it. Pokemon may be pets or battlers, but most of the time, they aren't shut-ins.
I know, it's kind of splitting hairs, but it's hard. I must say, though, that I don't care. I'm a nerd because I like them both in their own way, though Yu-Gi-Oh! is probably closer to my heart for various reasons.