Decent writeup:
http://www.nybooks.com/articles/2014/11/20/why-innocent-peop...
tl;dr: the current system incentivizes defendants (especially poor ones) to plead guilty regardless of innocence. This is caused by a combination of prosecutors/judges trying to be "tough on crime", overloaded public defenders, excessive bail, mandatory minimums and several other things.
I don't think plea bargaining is absolutely unfixable or evil but I also don't think it's a well-functioning part of the system as-is. I believe this is one of those cases where removing an option might be better for the justice system as a whole.
It's not even a case where removing an option can have good global effects; if you remove plea bargaining but change nothing else, all that accomplishes is that disadvantaged people get railroaded harder, and choke up the courts even longer as they play out their lopsided trials.