Claude/Sylvain, Claude/Hubert, Annette/Flayn, and Mercedes/Marianne?
Claude/Sylvain: Honestly, I'm a little disappointed we didn't get anything between them. I think we could have gotten a really interesting insight into both of their characters if they were to interact. I'd read fics of them.
Claude/Hubert: Okay, I have no idea which of these two would be the corrupting force in this relationship, but there's corruption of some personal level going on here and shenanigans from the shadows going on, and I need to see them scheming together.
Flayn/Annette: I'm really disappointed in the amount of supports Flayn has with the ladies. She's on my list of "characters in Three Houses that should have had supports with everyone" because SHE LIVES AT THE MONASTERY AND JOINS YOUR CLASS. I want to see her bond with Annette over magic and learning to use giant hammers together. It'd be adorable.
Mercedes/Marianne: Two of the most devoted soul who pray daily to the Goddess. And they have NO supports? They could have had something beautiful. Mercedes could discuss her own Crest related trauma with Marianne, and Marianne could find solace in a friend who understands her feelings surrounding her Crest and her prayers to the Goddess. They could have had such a beautiful interaction.
Or, as my sister puts it, "If these two were allowed supports we could have had a Protestant Revolution all across Fodlan".