Ok, so I'm not sure exactly how it's working, but mages that go invisible are usually revealed to me when I use True Sight or they simply reveal themselves. I can't be sure whether Non-Detection plays a part since I can't remember the battle logs for each battle, but I'm having no problems right now. Once enemies are visible (but still considered invisible for purposes of targeting), I can tear down their spell protections and then hit them with a True Sight to make them targetable by Breach.
Secondly, I am highly in favor of keeping Protection from Magical Weapons. It is essential to keeping enemy mages alive. Without that spell, they simply die to fighters since there is absolutely no reason to even tear down their spell protections if a fighter can just hit them. Sure stoneskin might take some time to burn through and such, but it makes the game far too easy which is not something I like given how easy vanilla BG is anyway. It is easily countered and fits as a 6th level spell.
Finally, I don't understand the complaints of people who say they don't want to carry around normal weapons. I thought this game's combat was all about thinking ahead, bringing the right items to prepare, and using your items to their full effect. A normal weapon can be quick-slotted so it doesn't even take up space in your inventory. And I don't understand the logic behind disliking the option to carry around normal weapons. If you hate them that much, simply go the long way of tearing down each and every mage protection which is easy anyway since you have so many more options in Spell Revisions compared to vanilla SCS.
Secondly, if you dislike carrying around normal weapons, why use your inventory for anything but loot? Normal weapons are not 'inferior' they are an alternative tactical option. Otherwise, stat modifying potions are 'inferior' since a caster can replicate the effects, wands and summoning items are 'inferior' because they are just mage spells in item forms, and heck, even scrolls are 'inferior' since they just take up inventory space to cast lower level versions of spells you could simply memorize! But we know that isn't true. Stat modifying potions are important since they allow instant use in battle to change stats like giving 50% magical resist, especially to non-caster classes allowing your casters to do something else. Wands and summoning items are useful because of their flexibility and allowing one to memorize other useful spells and scrolls accomplish the same effect to a greater degree. Thus, normal weapons are also a tactical option as valid counterplay to enemy mages and I don't understand anyone who wants to get rid of counterplay in favor of simply turning Protection from Magical Weapons into full weapon immunity.
Spell Revisions + SCS is already much easier than plain SCS so I would be opposed to any changes making the game easier.