Yes and no....Since Fowler was with OPR and OPR offered Neal and Kate that deal....Peter's career would not have been affected. Of course that plan didn't work out. If it had, we wouldn't have White Collar or we'd be stuck with Kate. 
The lie detector test Neal passed in In the Red was Sara's voice detector on a laptop thingey. It wasn't the same as an FBI polygraph.
Neal wouldn't have had Alex go to Diana's to steal the music box if Peter hadn't stolen it from the FBI evidence locker. So let's call that one a wash. 
Neal and Mozzie may have played a role in Keller's actions but it was Mozzie who stole the treasure and the FBI who let Keller escape (more than once) 
No one is flawless - not even Peter
I admit Neal is not flawless. If he was, he would be useless to the FBI and not as interesting as he is.
Edited to add: I don't know about Peter being in the clear for Neal running off with OPR's blessing. It was a secret deal; the paper work would have been buried, and I'm not really sure the deal was so cut and dry. I suspect Neal was going to be captured or killed, and then OPR wouldn't back up his deal. That would leave Peter with an escaped fugitive on his watch and care. His reputation would have been tarnished, and after everything with Fowler, he would have probably been fired.
I don't think it matters to Peter whether or not Neal could lie to a voice stress analyzer or not. The fact is that he lied and passed. And knowing how Neal is, would you really believe how honest he is? Really? If you were in Peter's shoes, knowing as much about Neal as you do...would you have believed him?
About the music box...Neal stole it AFTER he found out the truth. He was supposed to be working with Peter, remember? Instead, he decided to go his own way and have the box stolen. It's not a wash, because Peter was protecting Neal. Neal was furthering his own interests. There's a huge difference in intent.
With regards to Keller, I will once again point out that Neal did not take the threat of his presence very seriously. He seemed more irritated than alarmed at Keller's presence. And he was far more interested in saving his own butt -- and the treasure -- than he was with Keller. The FBI hasn't managed to hold onto Keller, but Neal, with all his awesome skills, hasn't managed to figure out a way to stop him either. So pooh pooh the FBI, but I'm not impressed with Neal's laziness about Keller popping back on the radar.
Wasn't it Sara's "voice analyzer test" that Neal passed and not an actual FBI lie detector? He spent about 5 minutes with it and answered approximately 2 questions. In "On Guard", Peter asks him questions for five hours with a standard, FBI issue lie detector. I really don't see any comparison, and it's just one of the things I don't understand/like about season 3. I could understand Peter's reaction to the test if he were only able to ask Neal a couple of questions before he got interrupted. I don't know why the writers had Peter question him so long and still not believe him. For me, it made Peter look like a some kind of a lunatic.
As far as who is to blame - I blame the writers for taking my favorite characters and making them all behave stupidly. I can't wait for Tuesday's show, but I also can't wait for this whole mess to be resolved.
I don't think Neal was hooked up to the lie detector for five hours. The responses would have been so wild after an hour that none of them would have been reliable. I think Peter interrogated Neal for five hours, but again...knowing Neal's history, why is it even a question of why Peter would bother to believe him?
Even if Sara's test and the FBI test (I don't think the FBI test is better...it's really more about the questions asked, and Peter didn't ask the right ones) are not similar, Neal planted that seed about his ability to lie through a test. It may not be fair, but again, that's his own fault.
I think that the characters have been excellent this season (with the exception of the episode "Scott Free", which I refuse to admit is even canon, and of course, Sara). I like the tension, because if you actually pay attention, under that tension the bromance still exists. Peter and Neal still have each others' backs for when it counts, and that's really what's important. I don't need them to be arm-in-arm and happy with each other. In fact, in Season 2 I thought things were getting a little ridiculous. It was too early for them to be that comfortable with each other. In RL, no, it would have been fine, but not for a tv show that needs to continue on for several more seasons.
I do agree that Bancroft appears to be the head with Hughes next in line. Hughes office being in the White Collar Unit may just be to give him more screen time.
But Neal didn't break into Sara's house, Mozzie did, so he wasn't lying. Sara's test was actually a voice analyzer and not a polygraph, so that's not really an even comparison.
In The Pilot and in Threads, I think it's 'understandable' to see Neal trying ways to get out of the anklet. After that, the only time he tried to get out was to save Kate. Then came the treasure and the accusation from Peter. Neal has 'withheld' information from Peter, which many can say is the same as lying. But Peter has also lied to Neal and withheld information as well. They both gave each other reasons to doubt. Peter is the FBI agent who tells everyone that he keeps his word and can be trusted. Neal is the conman who lies for a living. I would expect more from Peter than Neal simply because of who Peter is and what he represents.
The closest that Neal ever came to a blowout with Peter was during Hard Sell at Avery's party. That blowout was nothing compared to Under the Radar.
Sara asked Neal if he know who broke into her house. He said no. So he flat-out lied to her then. And as I said above, Neal planted that seed of doubt in Peter's mind.
I didn't say I didn't understand Neal's reasoning. I said that Neal was planning to betray Peter, and it wasn't for Peter's benefit. Neal got angry at Peter, but the circumstances for the accusations were totally different. Neal hadn't just been kidnapped, dealt with the fear of the explosion (Peter had agents and Neal to worry about), seen his partner held at gun point, and then be forced to kill a man.
The emotional circumstances were completely different.
And again, I'm not saying Neal was necessarily wrong for feeling the way he felt. I'm saying that Neal is not so innocent. Also, Neal is a big boy. He is responsible for his actions -- just like Keller. So if you don't want to lay the blame at Neal's feet for Keller's actions, I can't imagine why you'd blame Peter for Neal's actions.
Edited by Surreal44, 14 January 2012 - 11:59 PM.