I suspect you'll get more damage from the Apprentice, since max magicka has two purposes (casting spells and spell damage), where as spell pen only has one purpose.
More magicka since it helps both sustain and damage and does not depend on the actuall resist of the target.In the current state of the game Spell penetration can be actually completly useless when facing some guy with so much nirn that you can`t reduce his resist to the hardcap.
Spell pen imo. I tested the 2 stones...but that test was on mobs though lol.
However, I've got over 16k spell pen with light, nirn weapons and the apprentice mundus and my damage on most players is pretty high. 15k+ Dark Flares and 19k+ Prox Detonation crits.
DEPENDS on your class, if sorc use max magic, if anything else use spell pen
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Assuming you also use gold nirnhoned staff or dual wield, and 5 light armor: if target resists is above 50k apprentice is useless. If target resists are around 25k to 45k, apprentice is best option by far. Below 25k i'm unsure whats best.