Combat: X > 2 > 3 > 1
World/exploration + area music: X > 2 > 1 > 3
The rest of the music: 3 > 2 > X > 1
1st half of the story: 1 >>>>> 3 > 2 > X
2nd half of the story: 3 [Ch. 5-6] > 2 >>> 1 > 3 [Ch. 7] > X
Characters: 3 > 1 > 2 > X
Sidequests: 3 > X > 2 >>>>> 1
Overall, I'd give each entry a 9/10, for different reasons. X has by far the best gameplay/exploration, 1 has the best opening half up through prison island, 2 has the best conclusion and villains, and 3 has the best emotional moments and sidequests by a country mile. They each have their strengths and weaknesses, so I'm not surprised seeing different people with different values loving or hating different entries. I think 3 probably has the broadest appeal, though, and it's probably my personal favorite of the three main entries, excluding X.