I, personally, think that something as basic as facing in the direction of the enemy should be part of the challenge. I can see why they removed it in the 90s, when people were only just playing 3D games for the first time and didn't really have the controllers to navigate in 3D well, but is facing the enemy really something that we need to be hand-held through in 2017?
I don't believe that there's as big of a difference as you think. Most of the time, in 3D games like OoT, you're attacking an enemy who's on the same plane as you (i.e. not above you or below you). That plane (usually, the ground) is 2D. The perspective may be in 3D, but you're still controlling your character on a 2D plane. A 3D game like OoT pointing you towards the enemy really isn't that different than the idea that a 2D game could, similarly, point you toward the enemy.
It does more than just focus the camera on a target. It also faces your character towards that target. Unless you're too far away or the target dodges, your attack will land, all without requiring any aim on your part. I just think that aim should be important in 3D combat or else it's not really 3D combat. Z-targeting reduces 3D combat almost to 2D combat, since it takes away the challenge of facing the enemy, something which rarely was an issue in 2D games. That is, after all, essentially why it was invented: to make 3D combat simpler and more familiar to gamers who, at the time, were used to 2D combat.
The "gigantic problem" was not with 3D games, but with console controllers (at least the ones in the 90s and 00s). Z-targeting was never introduced or needed in PC games because PCs have always had separate controls for look (with the mouse) and movement (with the keyboard), making it much easier to play 3D games. More modern console controllers have incorporated dual analog sticks, which can achieve much of the same control, so z-targeting shouldn't be necessary any more. It's a feature that should've been retired at least a generation ago, IMO.