Just because you have to directly control the pet now doesn't mean it's no longer there.
At that point it is pretty much as the new DRK skill, the Inner Shadow. I have seem complaints that it is little more than a glorified DoT, and I can't hardly debate that claim. It acts on its own, regardless of your input, and does prefixed skills. We are not at that point yet, thankfully, but we are getting dangerously close. We hardly have to concern ourselves with out fairy anymore, and if you changed its skills to function around the SCH, very little would change on the actual gameplay of the class. The only remaining management we have is its position. This feels like shit when you take into account how important was the fairy on the job quest, being its own character. Loki's feelings are on point with this, it hurts the "class fantasy" that has been established. This is another layer hurting the enjoyment of the class, and while it may seem irrelevant to some, do not underestimate its importance.

SE decisions are puzzling, and at this point I think there is a hint of insincerity about why they made their decisions. If I have to venture myself to do so, this was a very poor attempt to make healers more accessible and easy to balance, but instead screwed with so many elements that made so many people love their classes while not addressing any of our complaints.