So Sophia Nashor basically just took everything that made our MC unique and made him even more boring. 1)Her proficiency with magic is just slightly less than his, so she'll be able to catch up with him given time. 2) Her mana amount is more than his. 3) His wands which boost his power more than usual and make him more unique can likely have their effects replicated given proper research into her affinities with wands.
In conclusion, the MC's individuality is now almost entirely gone, and it's only the third chapter.