It's because his face is more or less an amphibian face - very broad and flat, and utterly unlike what you expect in a reptile. (Toothless' design being wildly different then all the other dragons doesn't help either).

It's also an incredibly expressive face, but nearly all the expression's done with the eyes and the "ears" - they even lampshade it when Toothless tries (and completely fails) to smile.

And to round it out, Toothless has a fundamental dichotomy going - he's a very silly creature, but also an amazingly fierce one when he gets mad.

All of that, added up, makes his face damn hard to draw.

Looks great. I especially like the bottom right sketch. :)