I totally agree. Outside of both shows are centered around children playing a kind of game, I don't see a lot of similarities between the two. I can't really compare the games themselves since I have played Yu-Gi-Oh! before, but I've never played Bakugan. I've watched most of the series and I have still yet to understand the all of the rules of the game, mainly only the basics, while I got a good understanding of Yu-Gi-Oh! in the first few episodes, even though that first season, you can argue, didn't have much of any rules.
As a show, Yu-Gi-Oh! is much better. I feel like it has a stronger storyline, stronger characters and better character development. Bakugan is overall enjoyable, as I mentioned before, but it isn't as enjoyable for me compared to watching an episode of Yu-Gi-Oh!.