Despite their strengths, Treefolk suffer in a few areas.
Their Rapid Growth ability - for all the benefit it gives - doesn't function when the unit rolls an SAI, even if that SAI serves no purpose during the roll in question. This punishes certain units and really hinders the power of the ability.
Replanting is a useful ability as well, but the fact that it is limited to only ID rolls makes it much weaker than it could be. It often feels like a small consolation prize rather than a true faction ability, which is a bit of a shame for an ability that has so much potential.
Their missile units lack the targeted Bullseye SAI which is a critical piece of a missile strategy. The Volley SAI just doesn't do enough to offset the direct-damage and re-roll that Bullseye would provide.
While they can do a lot of work controlling terrain and protecting themselves, their mages have no offensive capabilities. They don't have access to any spells that function similar to Finger of Death, Lightning Strike, Hailstorm, or Firebolt.