I have a few valid reasons to back up my assertion (the topic name, of course); this is not just me complaining because I hate manual controls. I do indeed hate manual controls, but it is not because I am a noob, either. I will explain.

First, anti-air is primarily a role performed either by other carriers or by destroyers. Destroyers, as you well know, are the type of ships new players are required to play before they can expand into other trees. Expecting new players to use manual controls without any form of practice course (which existed in NF1, and I thought it was extremely useful in teaching the manual control scheme and aiming techniques) is unreasonable. Not to mention the fact that I largely believe manual controls to be wholly unnecessary on a DD. Yes, your turrets turn and reload faster, but the accuracy boost at short ranges you'll be fighting at is questionably useful at best. 

This brings me to my next point... I am 23 years old and I've played games since I was five. Not edutainment games, real games that require mechanical skill, like Doom, Quake, Unreal Tournament, TFC, etc. Not to mention I also played NF1 extensively and got quite good at manual controls in that game. This is my personal opinion, but I believe my opinion to be qualified: frankly, the manual control scheme is just awful. It's just bad. The loss of control that you suffer from being FORCED to use the right-click to move function is inexcusable in a fast ship like a DD. Now, this isn't actually wholly a bad thing in the grand scheme of the game; I kind of like the idea of players in heavy cruisers and battleships suffering a loss of fine motor control in order to more precisely aim their shots. However, expecting even experienced DD players to do the same is just unfair when movement is core to their survival and effectiveness. I believe the manual control scheme is a trade-off, not an "upgrade" to using Auto that everyone transitions to eventually on every ship. Yes, every control scheme can be mastered, but that doesn't make them all equal.

Thus, since DD players (and some CLs) are the ones performing anti-air duties... it seems rather counter-productive to force DD players to use manual controls just so they can hit aircraft, which requires MUCH more skill than the carrier player on the other end simply pushing a button to raise or lower his craft's altitude.

EDIT: I thought up a decent solution to this problem. I think the AA should work just like depth charges; that is, you set a level for the flak to explode at between 1 and 15, and the guns adjust elevation to have flak explode at that level automatically in Auto mode. I don't see why these two weapons can't be streamlined together.