None of those points really have anything to do with plea bargains -- they are just bad things about the CJ system.

-If the CJ system gives out indefinite punishments for trivial things, that's a problem unrelated to plea bargains. The solution isn't to make things even worse by allowing prosecutors to abuse the extreme sentences to force people into (sometimes false) confessions.

-Why should someone get years of freedom over someone else because they were law-savvy enough (or paid someone law-savvy enough) to realize they were going to lose and gave the prosecutor a sweet deal to make his job easier? Why create an even more uneven distribution of sentences based on who understands the system or can pay a lawyer to understand it?

-The court is set up to be run by humans; they can take mercy on whoever they like. We've chosen to set up our laws that way and I'm pretty ambivalent about whether or not that's a good thing. But even so, that's after the court has found that they are guilty. Mercy can only be applied after guilt is accurately and appropriately assigned -- something plea bargains make impossible. They induce false confessions (it's often the case that an innocent person would spend more time in jail waiting on their trial than they will if they plea bargain -- many decide they don't particularly like jail and take the plea. Not to mention the threat of a bigger sentence). They distort the findings of the court as prosecutors do not try to jail the person for what they can prove they did, rather they use the potential threat of what they might be able to suggest a person did in the future to provide the punishment.

-The law is always capricious and unreasonable. It is a human institution and it's adversarial. If someone is given an unreasonable and capricious sentence it's the fault of the prosecutor who pushed for an inappropriate charge (and happened to win anyway), or the judge who abuses his power to punish the person, or the lawmaker to design laws with appropriate punishments.

Plea bargains can make punishments more consistent and predictable -- everyone is guilty whenever they are accused. Their sentences are milder than technically could be possible but guilty nonetheless. For the unlucky few who have the audacity to maintain their innocence in the face of a prosecutor on the attack, well, capricious and unreasonable is exactly the name of the game. The phrase "throwing the book at you" exists for a reason.

The real point which I don't think you touched on is the simple principle of the government giving citizens special rewards and treatment for waiving their fundamental rights. It shouldn't happen if rights are to remain rights. Why shouldn't congress pass a law saying no taxes for people who sign a pledge to give the government permanent permission to search through all of their documents, computers, affairs, so they waive all protection against search and seizure? It's purely voluntary. Why should citizens subject themselves to the capricious and unpredictable execution of search warrants when they can just come home one evening to a police officer politely saying hello as he rifles through their closet? It's much better than a ridiculous unpredictable SWAT raid at 4am. And they get rewarded for it!