I really do wonder how you can feel that way. Have you tried playing the older games after ACIII? You lose so much control with the new scheme as the game decides what is best for you when it comes to where you jump and climb and which enemies you target. The problem is, the game frequently fails to match up with your intentions. This makes any frantic segment in ACIII and ACIV an effort in pure frustration, as things are bound to go wrong.
In the ACII games, you chose where you would jump. One extra button press to initiate the jump does not make it unintuitive in my book, especially when it gives you actual control over your character instead of leaving pretty much letting the game play itself as you hold the R trigger and press forward while hoping for the best.
It's even worse in any kind of combat scenario, as you can't reliably choose which enemy you're going to attack. The lack of a lock-on really screws you over in situations where you're supposed to assassinate a specific target. I'm just remembering the optional goals of "air assassinate target" or "use rope hook to assassinate target." Yeah, good luck doing that while your target is walking around on a crowded boat. There's very little chance that the game will decide to let you attack your target when you want it to.