The games I played are 1, GBA CoM, 2, re:coded, and 3. Haven’t played the Final Mix version of 2, and thus not the highest difficulties, so I can‘t comment that much on the combat system whether it’s as good as everyone says it is. The level design of that game though, I really didn’t like it as much as 1 or 3 as exploration wasnt as good. Both versions of CoM have an interesting card-based battle system not seen elsewhere, and the original has lovely pixel art. Haven’t played any other KH games with the command deck system, but I had a lot of fun with re:coded. Heard that the other command deck games (BBS and 3D) aren’t as good gameplaywise nor are the actions as well balanced, so I’m in no rush to play them.
My favorite would be different depending on what aspect we’re focusing on.
Visuals: GBA CoM, because it’s 2D graphics are ageless and pleasing to look at.
Story: 1 and CoM because that was before the story became so much more convoluted. Even though the latter pretty much started that trend, I still enjoyed the plot.
Music: Dunno. All the games have really nice soundtracks.
Combat: I haven’t played 2 Final Mix, so I’m not confident about assessing that. In terms of mobility, I really like 3. As for customization, Sora’s story in CoM and re:coded offer a lot of options for your arsenal.
Level Design: 1 and 3 for their emphasis on exploration, but more so 1 for being more consistent in that regard. In 1, I like how learning new trinites encourages reexploring old worlds. My favorite worlds in 3 are giant sandboxes where just roaming around is super enjoyable, but a good chunk of worlds are linear, with Monster’s Inc being the worst offender. Still, even most of the more linear worlds have multiple branching routes to get through them, so it’s not as bad as it sounds.
Worlds: 2 and 3. Most of the returning worlds in those games have some interesting differences such as the Hercules world focusing on different areas to keep them fresh, and the new ones are neat as well.
Overall: 1, re:coded, and 3