Here's a couple I would have liked to see in either game:

Houses:
* Edelgard/Mercedes: This one may seem weird because Mercedes is a devout follower of the goddess' teachings and Edelgard is almost the opposite of that, but I think Mercedes might be comfortable telling Edelgard about the happier times in her and Jeritza/Emile's lives.
* Raphael/Balthus: It'd be like the Balthus/Holst supports in Hopes, but replace all the talk about Hilda with talk about "the meats". Oh, and maybe an arm-wrestling/flexing contest or two for kicks.

Hopes:
* Monica/Petra: Maybe something about the two of them bonding over the fallout from the Dagda-Brigid war, their respective relationships with Duke Gerth, and/or their shared love of swimming/hunting.
* Monica/Constance: Monica helps Constance test out every weird magic spell she knows, and then keeps detailed records on the most useful/entertaining ones and how to replicate them.

I do like your ideas of Claude/Yuri, Constance/Shamir, and Annette/Dorothea. They all sound like they have lots of potential.