The issue with switching to the enemy with Manipulate is that they would now have to map controls to all of the enemies which might be too labor intensive. I think an easier solution would be to treat Manipulate like a Charm move, and the enemy simply starts attacking the other enemies instead.

The issue with Cover and Counter is that both moves would require the game to take over combat, which doesn't usually gel very well with an action combat system. An easier solution for both is that Cover is changed to Decoy, and the materia simply makes enemies target that user instead. Likewise, Counterattack could work if it was changed to be an input move for a successful block from an enemy, giving the player more agency and letting the materia add to the combat system instead of pulling you out of it.

Likewise, Long Range can be turned into a new ATB command when equipped that gives the player the Telekinesis ability from XII as well.

Enemy Skill is just the one I feel may be an issue. Even with the turn-based "pause" mechanic, I feel like SE wouldn't want the Menu screen to get too cluttered so I can see certain changes happening like higher tier spells replacing low tier ones for basic green materia magic, assuming they don't give each spell unique animations and function. If Enemy Skill is added into the game, I imagine several skills will likely be removed for space and that the method of gaining the skills would be changed. The easy solution would be to just borrow from FFX and have the default skill for the materia to be Lancet and then your character has a certain chance of acquiring an enemy skill when used.

The three materias I see having major issues simply due to what we know about the new system is the Counter Command, Magic Counter, and Sneak Attack materias because of the new process of magic costing ATB and MP to use, and that may not work if ATB resets between battles. We'll have to see.

Jump might still work if it was basically treated as a jumping attack instead of dragoon jump, so Cid can maintain his usual abilities. Like counter, I can see Jump working like an added move you can press a button to activate and then follow up with a regular attack, but again, I can also see none of the CC exclusive materia appearing at all.