Affirmative:

1) Plea bargains provide incentive to implicate innocent people
When criminals are provided with a choice between longer sentences and providing assistance, many do not hesitate to implicate innocent people

George C. Harris, "Testimony for Sale: The law and Ethics of Snithces and Experts", Pepperdine Law Reveiw
"Of the sixty-four cases of DNA exoneration analyzed by Dwyer, Neufeld, and Scheck, "snitch" testimony was a factor in 21% of wrongful convictions"

2) It penalizes criminals for using their rights to a jury trial
Criminals should not be told that if the want to escape some sort of punishment, they must sacrafice their rights. See "From plea negotiations to coercive justice: notes on the re-specification of a concept" by William MacDonald for cards about this argument

3) Plea Bargains are arbitrary
The decision whether or not to plea bargain is entirely in the hands of the prosecutor, as well as the concession granted for the bargain. Thus two individuals who commit the same crime will recieve different punishments, violating a standard based on the fair application of the law

Lisa Egitto, "Substantial Assistance Departures: Threat to Sentencing Goals or Necesary Evil?", St. John's Journal of Legal Commentary, "the cooperating defendant recieves lighter sentence than a than a similarly situated defendant who has committed the same crime and does not cooperate. This problem is intensified by the lack of formal considerations in place for determining the degree of departure. The degree of departure is left entirely in the hands of the sentencing judge, possibly guided by the recomendation of a prosecutor. This situation creates vast disparities in the sentences recieved by defendants

4) Plea Bargains violate proportionality
Another argument is that plea bargains do not reflect the culpability of an individual, and sometimes reward greater culpability.

Egitto, "Proportionate sentencing is the goal of both retributive theories of punishment and the Guidlines. Substantial assistance departures thwart this goal by reducing sentences for individuals who cooperate with the government without regard to the culpability of the individual"

Christopher Mascharka, "Manditory Minimum Sentences: Exemplifying the Law of Unintended Consequences", Florida States University Law Review,
"Those who are most able to offer substantial assistance to prosecutors-and recieve substantial sentence reductions in return-are high level, culpable operatives in the drug business. Lookouts, messengers, and other underlings who have little valuable evidence to offer, end up recieving the full sentence. This phenomenon-highly culpable individuals recieving shorter sentences than their periphial co-conspirators- has aptly been labled the "cooperation paradox" and "inverted sentencing."

5) plea bargains create a disadvantage for the defense attorneys
The U.S. depends on a adversarial court system- two equal lawyers will try and prove opposite sides of a case and The Truth will be revealed. However, plea bargains give prosecutors the ability to find additional evidence to prove people guilt without the defense having a similar ability (because the defense can't control sentences), biasing the system in favor of the prosecution.

Harris, "The process by which witnesses are selected for compensation in criminal prosecutions is asymmetrical in two related and significant ways. First, the option to compensate a witness available only to the prosecution and not to the defense. Second, prosecutors have no incentive to, and as a matter of practice do not, offer compensation for exculpatory testimony"
This can be linked back to some sort of due process standard

See http://ld-debate.blogspot.com/ for ideas about conceptions of justice