A related consideration, which is more about the methodology of studies claiming to measure human irrationality, is that the problem you think a test subject is solving is not necessarily the problem they're actually solving. I guess a well-known example is when you ask people to play the prisoner's dilemma but in their heads they're really playing the iterated prisoner's dilemma.

Right, this is an important point that could use more discussion.

In closer inspection a lot of the "irrationalities" are either rational on a higher-level game, or to be expected given the inability of people to "feel" abstract facts that they are told.

That said, the inability to properly incorporate abstract information is quite a rationality problem.