Which magic schools should I choose for the late game? Or should I go for a specific artifact?

In the late game (if you don't go for the Conflux), I would definitely choose Chaos. With prolonged gameplay involving spellcasting, there shouldn't be any problems, so the damage output will be high (naturally, combined with the Wizard's artifact, and possibly using new gargoyles to further increase the damage). For the second magic skill, I would choose either Darkness or Light. I'm leaning more towards Light, as you can find more spells in the guild, and boosting troops with mass spells is useful for the Academy, more than any other faction with their meager combat stats. There's also a chance that you'll find Divine Retribution in the guild, a spell that speaks for itself.