1. Ed and Al are both like Sora and Donald/Goofy. As they go through the game they meet up with other characters and if you notice, the battle system is almost the same.
2. The final boss, Crowley, reminds me of Ansom, the final boss of KH. They both have long hair (the colors are not that far off either, Crowley's is light and silver looking and so is Ansoms) and they both have similar attire (long black coats).
3. They are enemies that are created by both of them. Ansom created Heartless, while Crowley created Golems. Plus, they have an ambition/goal for creating them.
4. Both types of monsters look incredibly similiar. Although the Golems in FMA 2 are taller, one of them looks similiar to the new Heartless in KH2. The smallest version of the Golems look a lot like the Heartless monsters in KH (really big heads and small bodies).
5. They're both produced by Square Enix. Go figure.
Only difference is that the AIs in KH actually fight (although like to waste items a lot). Al for some rason just stands there most of the time if you don't constantly command him.