Magic systems in games I think is always going to be contentious. Its very very hard to please everyone.
BG2 gets close to having one of the best ever though - especially with the Sword Coast Strategems mod. Specifically what made it unique was the layers and layers of magical protections you could apply that you needed to know how to dispel. Stuff like being unable to cast dispel magic on enemies immune to abjuration, or being totally unable to deal with invisible enemies as they had illusion immunity spells applied (i.e. True Seeing wouldn't work). It was by far the closest I've seen a game come to making mages feel immensely dangerous. The flipside of course is made them wildly OP. Hard counters will always be contentious - see Josh Sawyer's talks on this, but for my money - BG2 was the best we ever got in this department.
The spellcrafting that the OP is discussing honestly is incredibly simplistic by comparison. We saw it in Morrowind, Tyranny, we saw it in Two Worlds 2, and in the Magicka games in a different way. None of that captures the reality altering abilities that a D&D mage should be able to exhibit.
Bottom line is that having a well curated list of spells is always going to be better than Spellcrafting.
