I might be biased in saying this, but by far, this is the best Yu-Gi-Oh anime of all time.
Yes, the first two seasons are slow and they did make some budget cuts in the animation department early on (Alexis and Zane scene). But overall, it's solid for it's time and the fact that it utilizes no 3D animation of any kind is marvelous and a huge problem with Yu-Gi-Oh 5Ds and onward.
I went a little off track there, apologies, but yes, the story isn't much to look at at first glance, duel academy with a dark twist, but after you unravel the past of the main protagonist Judai (or for you dub watchers, Jaden), you start to really get into the story, past season 2 of course. Don't get me wrong, the Shadow Riders had some potential, but were mostly underwhelming and the Society of Light was an interesting concept, but executed poorly. By far, the best arc of all of Yu-Gi-Oh, is the Dark Dimension arc. Which boasts some of the best villains and reveals most of the backstory of our protagonist.
Like I said before, the animation is your run of the mill Yu-Gi-Oh art style, though I have to commend them for not using any 3D animation, leaving us with awesome looking boss monsters who feel like they're right at home in the anime, unlike for example, Yuya Sakaki's Odd-Eyes Pendulum Dragon, which doesn't mesh well with the traditional animation.
All of the sub openings are amazing, showing the state of our beloved Judai slowly shift. At the start of the anime, you already know you're going to have a blast, but as you go on, you start to feel for the ops, which fit marvelously with the story. I'd say the same for the dub, but it gets old pretty fast, what with not including season 4 and the last bit of season 3, it doesn't show anything apart from a song that's supposed to get you pumped for the show, and that it does well. The idle sounds, incorporating an electric guitar, similar to the changing scene of an old Disney show, is also a nice touch.
Now then, onto the characters. I can't imagine a Yu-Gi-Oh series with a deeper and darker premise than Yu-Gi-Oh GX, if you try and say Yu-Gi-Oh 5Ds, I'll tell you to shove that power of friendship up your ass and watch all of GX. The protagonist is a blank canvas at first whose whole purpose is for us to put ourselves in his shoes. Meanwhile, the reason he's bland in the beginning is because of a traumatic childhood that I won't spoil in this review. My point is, yes most of the supporting cast did get pushed to the side, apart from Chazz, who had his arc and only then was pushed aside. But the reason for that is that his "friends" put him in the leadership position against his will and when the new student in season 3 arrives, along with the rest. (Fuck you Amon) treated him as an equal, of course he wanted to spend more time with him, again, no spoilers.
All in all, it's definitely worth the watch, yes, you'll have to watch the first two seasons, but once you get to the middle of season 3, you won't be disappointed.