Definitely Sephiroth and Cloud, their relationship was simply too bizarre, it was disturbing to see how much they were obsessed with each other, also Cloud was gay from the start...
Joke aside, Zack and Aerith were just adorable in Crisis Core, shame though their relationship was only for a short notice.
Zidane and Garnet are also a cute couple, it was fun to watch they way they treated each other the first two discs.
This also.
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