Why not use Slitherhead as a more resilient way of getting a counter on Sage of Hours? People won't be boarding Graveyard hate against a combo like this, and you have another way of getting a free counter.
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Free 2/2s plus free devotion for Nykthos. One burning tree allows you to activate Nykthos for free, so even late game with even moderate board position sets it off.
Playing in Modern, you should look out for Affinity, Pod and Tron. Ancient Grudge is a cheap option for targeted removal of artifacts, Deconstruct is free artifact destruction for an opponents pod, Batterskull or Cranial Plating. Fissure Vent would help against Tron, as would Acidic Slime. These are all sideboard suggestions, and unfortunately all are pretty reactive and some expensive, which may be working against the quick plan the deck has. Just some ideas.
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