Chain of Memories is reaaally close for me too, Stealth. It got a lot of hate for the card battles, but I got into the swing of things pretty quickly and I relished the challenge. However, Birth By Sleep beats it for me too. The Command Style system was a wonderful evolution on Forms, a switch to a recharge-based system that felt like a natural next step from the MP Recharge of KH II, and of course I loved playing as the new characters. Aqua was my favorite as the true battle mage, and I really connected with her character.
I suppose it didn't hurt that once I managed to make two Magic Hours and two Time Splicers, nothing stood in my way with her except the two secret bosses.