Again, no more so than for base stats like STR/DEF/etc. It's more difficult if EVERY encounter and abilities is assigned a SINGLE affinity, but it's really not a difficult mathematical problem no matter how you slice it. Strengths and resistances are one of the most fundamental mechanics of strategy games.
Yes, but you're neglecting the idea that elemental wheels often serve as a bypass to the strengths and resistance calculations unless it becomes a fundamentally accessible component.
If a character is weak to say, piercing, but yet is also weak to ice magic. Your Black Mage will take priroity over your Dragoon simply because Black Mage has less risk due to its access range and high performance floor. Unless there is something that would give Dragoons an edge additionally. At that point, you're designing your battle against your core components, rather than using them to accentuate or improve upon your core components. The designers are fighting themselves to tweak balance rather than making a more inventive and enjoyable battle.
Conversely, say that Ramuh is weak to magic, particularly Earth, but virtually immune to thunder, and you've pushed Black mage out in favor of the current incarnation of WHITE Mage, simply because BLM's fire is going to be inefficient against a caster who can both DD and cure effectively because the elemental wheel comes into their favor.
They would have to play against their own designs in this case, basic building blocks of strategy games or not.
Removing the Elemental Wheel is in this case removing the fifth wheel on a car. The Elemental Wheel wasn't functioning to any real beneficial effect in 1.0. Factors that balanced out the inequities of magic were being applied to ALL magic types and elements. As well as the components in the encounters that encouraged magical usage or gave them a specific purpose. And these methods were more inventive than "Use Fire/Wind/Ice." Though that can still be applied in more specific cases, likely having more than one trigger. It's just no longer a default requirement to be efficient in a fight. Which is good considering PUGs will be managed primarily by computer sorting with Content Finder. Trust me, you don't want to end up cursing the twelve that you got into a Ramuh fight with a Black Mage who's decked out their thunder spells and is just trying for his Judgement Staff.
The fights themselves will be plenty deep without the elemental wheel. They were with Garuda, United We Stand, To Kill a Raven. These fights were just the right level of depth to encourage team-based play without hamstringing people. Most especially United We Stand which I say has been the best feeling fight encounter I've had in a very, very long time. There were multiple effective means of getting that fight done with multiple different set-ups. It was challenging enough to have things go wrong and force you to understand what exactly was going on, and the truely skilled it was just a blast to rip through even if you dominated it. And the elemental wheel had absolutely nothing to do with it.
So I really do not mind them reducing the variables they're forced to control in this sense. There is plenty of ways to add depth to the combat that doesn't involve arbitrary stat manipulation. And the system of weaknesses and strenghts can still apply without the elemental wheel. Hopefully they're more context sensitive than passively existent as well.