My thoughts here are not related to any reasoning about balance changes - this is really only to share opinions about the concept of antimagic and whether people are still interested in that at all. I am fine with the decision to remove the skill which was taken long ago. And honestly, I don't have a clue about the current state of magic vs combat balance. (One advantage of close combat is that you can benefit from extremely rare items, while a red mage does not get all that much from three ruby encrusted items of talads arm - but now I am getting off topic.)
Concerning stacking with other ways to resist spells: No changes there, you could either train a magic skill or antimagic to get save throws, but the effect would be the same - with the notable difference that antimagic ruins your career as a mage.
LigH: I am not aware of any fixes or abuses, but as a side note, training body development is one of the exceptions where the low skill ranks can really help you, not the high ones.