1. Snow/Hope. I don't see how it's even possible to really like one while disliking the other since their character arcs blend together so much and they are basically dependent on each other for character development and growth.

They were easily the best and most sympathetic characters in the game. Snow is a braggart who has to come to terms with what true heroism is and Hope has to deal with the typical misplaced anger that almost always accompanies sudden loss. They both mature a lot together and the scene where Snow carries Hope is one of the best in the game.

2. Sazh/Vanille. Aaother pair that is so connected that it's pretty much impossible to imagine liking one and not the other. Their interactions are great and they had possibly the most emotionally intense scene in the game.
Vanille is also a total cutie pie.


And then there were the rest. I think one was Claire Redfield and I always really hated her. The other kept going "UhhhhHUHHHHHHhh!!" in battle and that's all she contributed to the game. Top notch Resident Evil level voice-acting there.