I don't really like Pokemon now, but Yu-Gi-Oh was plain horrible

I prefer more Pokemon than Yu-Gi-Oh.
Though the first seasons of both were my favorite.

I watched both when I was younger, and I have an aversion to each now, so the decision is difficult. Both of them had their good points and their bad (the dialogue made me cringe sometimes).

What it comes down to for me is, which one actually gave me a reason to want to play the game? Pokemon certainly managed that - all the colorful animation and interesting tactics really made me want to be the very best. As for Yugioh, I was playing the card game at the time, and I just kept getting frustrated - not with the game, but with the show. I liked the game, but the show portrayed the same cards with the wrong abilities. It just got to me in a big way.

Putting the shows aside...

I've played Pokemon since its inception in America, and though it's had its ups and downs, I've thoroughly enjoyed the time I've spent playing it. Yugioh just never appealed to me in the same way, unable to satify my desire for rpgs. Plus, the Pokemon Adventures manga made up for where the anime lacked. And so my vote is clear.

Pokemon in its first series - I didn't like it after that. Basically, I liked both of these shows and watched them when I was a kid, however, Pokemon is more of a favorite, as I really enjoyed the show and it was the first proper kids show I began to watch after I stopped watching ones aimed at a younger audience... also, Yugioh was alright, but I got over it very quickly.

In fact, I've played a lot of the Pokemon games over the years and casually enjoy them, while Yugioh games really just bored me. Lastly, the idea of a show where you had little pet animal/creature things (or pocket monsters) was pretty revolutionary, while Yugioh seemed to just adopt a similar idea, then add cards to make it seem cooler to the younger kids that don't understand the idea of pinching things from another show.

All-in-all, Pokemon - 1 and Yugioh - 0.

Having watched 5Ds and around 50 episodes of Duel Monsters, I have more of a history with Yu-Gi-Oh. Whereas, I've never actually sat through an episode of Pokemon.