So what is Pythium's weakness?

Being sacred isn't all that overwhelming of a cost difference.

With your ability to Heal and your Mystics versitility you can make much more in the way of SC's. (Golems, etc) And equip them properly. Arco is no slouch at all when it comes to dealing with Pythium.

Use Astrologers to Pre-Doom his large armies then use your own Wrathful Skies/Returning Mystics to cripple his forces.

Your higher end Astral Mage (Astrologers) cost much less so you will have more than he will, allowing you to duel him more successfully.

Don't forget that Elephants if used in high enough squads won't rout, which will destroy ranks of infantry and cavalry (until his mages get at them).

The pretender will be your key factor and how you use him.