There is much evidence to support Zoe's supremacy, having potentially demonstrated at least four of the Seven Wonders; nearly as many as Madison. She may have manifested Pyrokinesis as early as the first episode. When she thought she was going to be stabbed by the other girls, the candle flames reacted. Outside of Misty, Zoe was the first of the witches to be able to bring life back to the dead (Resurgence), resurrecting Kyle when spells failed. She subconsciously undid Marie Laveau's voodoo magic, returning her zombies to their original lifeless state (Vitalum Vitalis) and casting her to the ground. Whatever she did was enough to surprise Marie Laveau; who claimed the witches have some real power in the Academy (now). Zoe also subconsciously chose the right book to expel the Axe Man's ghost, having being unknowingly led to the Ouija Board that both summoned him and revealed Madison's fate in the same episode. Finally, she has demonstrated Telekinesis, summoning a knife to stab the Axe Man in the penultimate episode.
Arguably, it would be fitting to close with Zoe's ascension to supremacy. She has championed the coven and tried the hardest to unite the witches. The series opened with Fiona's sickness and the first manifestation of Zoe's power. When Zoe arrived at the Academy, the others appeared to have been living there for some time before her arrival, increasing the chances that she was responsible for instigating Fiona's illness. There has certainly been enough foreshadowing for it not to come left field.