Here's my idea to the devs on how to bring back auto-firing without interfering with other skills. Do what every other MMO does and add a hidden skill queue. If you don't know how it works, I will explain it.
The skill queue only needs to hold 2 specials. The current one in use, and the next one to use. At the start of combat, the player triggers it by activating an attack. That attack goes into the queue and executes, and the cooldown timer starts. At this point, the queue is empty and the character is doing nothing.
If a player were to choose a different skill, that one would activate and fill the first slot of the queue. When the player chooses an attack while the first slot is filled, that attack goes into the second slot. When the first empties, the attack in the queue is moved to the front and executes. At this point, if the auto-fire skill is ready, it is automatically added to the second slot of the queue.
When the skill that has auto-fire is done the cooldown, the auto-fire will check for an open slot in the queue. If the first slot is empty, the skill is added to the first one and executes. If the first slot is filled but the second is empty, it is added to the second slot and waits in the queue. If both are filled, it does nothing and waits for the second slot to empty.
If both slots in the queue are filled and the player chooses another skill, that sill will replace whatever is in the second slot.
For the UI, a highlight can be used on the icon being queued to show the player that that skill will be the next one to execute when it is possible.
Players get their auto-fire back and the problem with trying to time the skills is solved.