NOT JESSE X JADEN NOT ZANE X ALEXIS NOT BLAIR X JADEN AND NOT CHAZZX ALEXIS
JADEN AND ALEXIS ARE THE PERFECT MATCH in the end those two will end up for sure and Jaden's just immature of his feelings towards Alexis time will come when Jaden will notice his feelings towards Alexis
My former answer was Jesse and Alexis, which I had as my favorite Yu-Gi-Oh GX couple 4 years ago. My interest in this pairing faded only a few days/weeks later. Since then, I didn't like any pairing in this anime.
It wasn't until last year when another pairing caught my attention.
Jesse and Jaden.
Even 4 years ago, I couldn't deny how important Jesse is to Jaden.
The fact that Jesse's disappearance ended up with Jaden having a mental breakdown, causing the "deaths" of his other friends and becoming so depressed that the Supreme King took control over him shows how important Jesse is to him.
Not to mention that Jaden hasn't acted like this before. His other friends have been in trouble a lot of times, both before Jesse appeared and after. Yet, Jaden has never acted like this. He cares about Jesse more than he cares about his rivals (Chazz, Zane, Aster), more than his friends (Alexis, Bastion, Chumley) and even more than those who are like brothers to him (Hassleberry, Syrus).
As much as I try not to ship this pairing (Which isn't going that well), there's no doubt about it; Jaden has a special connection with Jesse that he doesn't have with anyone else. Not even with his cards.