These are both the second anime generation of their respective iconic multi media franchises. Whereas Pokemon Advanced Generation (as well as pokemon in general atm) follow the same protagonist and mostly the same characters, GX has a entire new cast of heroes but we do get to see many cameos from the classic cast. Both are still however direct sequels taking place in the same world shortly after the events of the previous anime generation of this series. Both shows partner their heroes with monsters to battle/duel with friends and renown opponents. Both heroes only seek friendly competition but often clash with the forces of darkness to uphold their morals and do the right thing. Both have amazing art styles, OST's & character/monster designs. read more
Both anime follow young protagonists who want to become the best at their fields. In both anime, the protagonists often make new friends and rivals, while battling other characters using monsters that have special abilities. Overall, both anime explore similar themes and have a similar mood.
In both anime, there is a young protagonist who sets up to become the best at his field: Yugi tries to become the best duelist, while Ash tries to become the best Pokemon trainer. Also, in both anime, the main character engages in duels with other characters using their monsters: in Yu-Gi-Oh!, the monsters are summoned through cards, while in Pokemon, the monsters are summoned through Poke Balls. Both anime show the adventures of these characters as they make new friends, but also new rivals.
Both are shows targeting mainly on kids. The main hero is a young boy who obtains some creature/hero contained in some device (pokeball/disk) and battles with said creature/hero against other device owners.
Pokemon and Medabots are shounen anime and they pretty much alike. Both anime's are about a boy, who lives alone with his mother, that gets a pokemon/medabot as their partner. They become friends and battle a lot with other people. They wanna become one of the best and to do so they participate into competitions. Both series also got some "bad guys" and they are complete idiots, they always lose in the end.