Yeah, X and Zero would get my vote too.
In Classic, it was a lot more light-hearted with a goofy villain vowing revenge before flying off at the end and the hero going home to an extensive family. X didn't have that. He doesn't have a family or even a home as far as we can tell. He came into an unfamiliar world all alone apart from some conversations with Dr. Cain that exist solely in the X1 manual. The only familiar face and kindred spirit is Zero, and given Zero's loner and more abrasive personality, the reverse appeared to be the same for him. A genuine friendship rather than the acquaintance / friendly rivalry relationship he had with someone like Colonel. And there was a lot of faith and trust between them like Zero sacrificing himself to stop Vile because he knew, for no particular reason other than faith, that X could defeat Sigma on his own. And again in X2 he opts to let X take the much more dangerous objective of fighting Sigma. The Xtreme games on GBA, particularly 2 had a lot of the two acting on their own knowing the other would be self-sufficient.
My favorite aspect of the Day of Sigma short, aside from X remembering his few conversations with Dr. Light before going full on Shining Finger on Master Maverick Asia of the East, is the movie is just a buddy cop flick staring X and Zero.
Runner up would be Phoenix Wright and Miles Edgeworth from Ace Attorney. Again, so much trust and respect between the two of them and like any good character relationship, they actively make each other better for knowing one another. Phoenix helps Edgeworth rediscover his compassion and Edgeworth helps Phoenix channel his altruism for tangible results. I'm never going to forget the first game how effectively and naturally the attitude toward Edgeworth changes. At the start of the final court day of the fifth case, Maya is gone, Ema is gone, Gumshoe is gone, Lana is gone, and you're all alone. It's very unsettling but then the person that speaks with you before court opens is Edgeworth and I threw up my hands and went "Yoooooooooo!!" I just took the moment in how when I first met Edgeworth he was an asshole that I hated and now we were full on bro handshake.
And of course you have the fun moments like
KISS, DAMMIT!!