I dug up some interesting papers of criticism on orthodox economics the other day. All papers are written at least a decade ago, but after I read them, I think those relevant problems still exist today.
Mark Blaug's Ugly Currents in Modern Economics cast some doubts on the following issues. Whether General Equilibrium theory make us understand more of how actual markets work; whether Game Theory infuses more novel observations in IO economics; Whether different schools of Macroeconomics are more and more suited to explain how the world actually works; or whether Friedmanian view of positive economics need injection of "assumption robustness" rather than merely overlook the realism of assumption and only take perdiction accuracy of a theory into consideration.
Another paper is written by former dean of MIT Sloan school of management Lester Thurow, namely The Strengths and Weaknesses of Economists. Although Prof. Thurow was not a academic economist, his points are quite illuminating. All the doubts are important questions for us to learn and discuss.
The two papers above are published in a less academic journal, thus their impacts would be limited. As I looked into more prestigeous top academic journals in economics, the voice of critics became weaker. However, there did exist a heavyweight in orthodox economics arena who made his criticism more influential. He is D. N. McCloskey.