The problem as I see it is that Pyramid has a lot of extra interfaces and support for things in the core by default (and some concepts that are completely missing from most frameworks like context). So much is there that it's easy to lose sight of how little is actually required. Fundamentally you can write Pyramid apps in 10 lines of code exactly as you would with Flask but that's less interesting for bigger apps and so the docs focus on all the extra features.
I mean if you take the example at the top of http://docs.pylonsproject.org/projects/pyramid/en/latest/ and add in the pyramid_jinja2 library via config.include('pyramid_jinja2') then you basically have views and jinja2 rendering fully baked.
As in the previous example if you get right down to it Pyramid doesn't even have a templating engine! Flask comes with jinja2 built-in! So scaling DOWN to APIs where this is not necessary is an interesting thing..
By saying "it's not a particularly opinionated framework", I mean to say that it allows you to add, easily, whatever you want to it. However, there is a fair amount of conceptual load in doing so. The difference between a flask app and a pyramid app with pyramid jinja2 built in is that one of them takes about 20 seconds to understand.
Don't get me wrong -- I think pyramid is fantastic. But it it is disingenuous to suggest that there are not differences in complexity between the two frameworks.