It looks like there’s an upper limit to how many inputs a material can have and we keep hitting it. The good news though is that all of the very slow, optional features are now switched and so the shader will recompile without those branches as needed. This means you get similar speeds to the earlier versions of the shader by switching off watercolour, etc.
My general feeling is that this is becoming more of a next-gen effect in some regards. At its most basic the cel shading does a fine job and is fast and suitable for current and last gen hardware. With some of the really nice effects you do need a modern or high end card though. I think there’s ways to improve this since the slow features revolve around custom blur functionality, but they’ll require some research.
For those of you that have access to the pre-release repository, those changes are now on the master branch. Not all the presets have been updated yet so some of them will undoubtedly look whack.
This release also forces UE 4.9 support. I haven’t tested it but I expect this is the new version cutoff.