I've a few ideas, some of which have already been mentioned...

Freya and Amarant would've been good, if you can overlook the fact that they belong to different species. But, like most of FFIX's characters, they got no development except for their interaction with Zidane, so there wasn't even a chance to see their friendship grow.

Quistis and Squall also would've had some potential. That idea's been quite well explored in the FFVIII forum, so I won't bother repeating the reasoning here.