Critics of the criminal justice system have been railing against the utterly lopsided plea bargaining system, among many other CJ issues that all serve to prop up the others. Some cursory googling turns up:
I haven't gone through every single one of these with a fine toothed comb but none seem to have a problem with plea bargaining itself - the root problems they describe are things like draconian sentences, overly broad prosecutorial discretion, outright fabrication of evidence, etc. The remedy suggested by the poster above - just getting rid of plea bargains isn't going to help in the cases described by these articles.