You know, the whole Kramer arc in WhiCo's S3 was really painful, especially in the light of S5, because in S3 Peter stood firmly against Kramer and by Neal - but in S5 he did exactly what Kramer had done to Neal, called him a criminal and told him he would never change. After everything Neal had done for him, Peter turned into Kramer. So in the light of that, watching S3 was even more painful.
And it was lotsa painful as it was, because Kramer wanted to take Neal away from Peter, he wanted to transfer Neal to Washington, slap the anklet on him indefinitely and threaten Neal with a life sentence to force him to work for him, Kramer, and only for him. It was one thing to make Neal serve his 4 years but a life sentence? Peter got so furious when he heard what Kramer had in store for Neal and that made him help Neal even though he wouldn't have done it otherwise, but he just would not, could not stand for this, for Neal basically being Kramer's slave for life. Because what Kramer wanted to do to Neal really was slavery, he wanted to take away Neal's free will, completely. Peter rather wanted Neal on the run than... this.
And at the commutation hearing... both Elizabeth and Jones really pissed me off. She wouldn't want Neal dating her sister? Really? REALLY? You might say many things about Neal, but when he loves someone, he would die for them. And she said THAT at his commutation hearing? Are you fucking kidding me? And Jones - he said that Neal was his friend but then he dissed everything about him. No, Neal was not his friend, he has never been his friend. He was just a tool for Jones and in that regard, Jones was no better than Kramer, because he has never seen Neal as a person, only as a thing that helped them solve cases, an additional computer or whatever.
Which is something that really pissed me off about this show in general - as much as I adore WhiCo: Neal helped the NY branch of WhiCo reached a solve rate of 94%! Unprecedented thing. And who got all the accolades? Peter Burke. Because in the eyes of the Bureau, Neal didn't deserve it, even though it wasn't until he joined the unit that their solve rate jumped 20+%. But that didn't matter to anyone, ever. Because Neal was just a CI. Only Kramer took notice - and he was determined to exploit Neal by trying to slap a life sentence on him so that the Bureau wouldn't lose him as a tool. Jesus! Yes, I feel very strongly about this because the FBI was using Neal to their benefit with not even a thank-you and yet they still made it sound like they were doing Neal a favor because he was a convict.
So yeah, after this and after how Peter behaved towards Neal in S5, I actually rooted for Neal to take off and it's also the reason why I'm very happy about how the show ended.