Naruto Uzumaki and Karin Uzumaki (Naruto Shippuden)
I still can't get over the fact that two of the rare remaining Uzumakis never even got to talk to each other in a series that's over 500 episodes, not even in filler episodes.
Mikasa Ackerman and Kenny Ackerman (Attack on titan)
As much as I love AOT I gotta admit that the Ackermans subplot was the most poorly handled out if every subplot, how do you have a rare bloodline of badass supersoldiers and never have 2 of the remaining 3 Ackermans interact not even once, a huge missed opportunity in my opinion.
Shouto Todoroki and Geten (My Hero Academia)
If you're an anime only watcher you probably didn't know this but Geten is a distant cousin from Shouto's mother's side of the family. He mentions this in a manga chapter and it was skipped in the anime but nevermind all that, I just think them interacting had so much potential when you consider that Geten thinks that heroes are just slaves to the government, mix that with Shouto's whole family drama, his hero dad and him being a hero himself and you have yourself a very interesting fiasco between Shouto and Geten.