My two cents here.
Starks:
Honor can only take that far, you know, and it is widely overestimated in general public. Good ruler is almost always a dishonorable one (Machiavelli).
I generally disliked Starks(Eddard, then Sansa, then Rob, and now Jon...) from the book 1 onward for two reasons: their "holier then thou" attitude is neither realistic for any person with any ammount of power, nor compelling for me personally (mainly because it is so boring...). They made so many mistakes I cannot even name them all. Starting before the timeline of the books, and following every single step of them(If anyone is interested - we can discuss this privately or in another thread.). Basically it was only their downfall was only the matter of time. They pissed off a great to many of people, while having quite too few powerful friends. The Red Wedding actually improved the Stark family chances of survival, because now they are perceived as martyrs and "Good Kings of Old Times", instead of honor-crazed lunatics they actually were. If Rickon is ever to be found - he will now most likely be supported by most of northern dynasties in his claim on Winterfell and the North. If Red Wedding did not happen - Starks would most probably be deposed for good. Irrelevant of actual war outcome.
Arya and Catelyn are quite nice, but Catelyn became a collateral casualty for associating with other Starks, and Arya, quite expectedly survived. Young Starks are not quite fleshed out yet, so they may one day become good rulers.
Danaerys:
Her "Plot armour" comes not from her personal characteristics, but from the fact that she had pretty much nothing at the start of the story and she still does not have pretty much anything. Also her companions are pretty good, and are in position where they MUST rely on her, for having very little choice otherwise.
She managed to lose her fertility, strong husband, child, initially friendly Quartz, her dragons(well, she may recover them, but it is still a chancy business), her ships(safe passage to Illyrio), in the procss of losing her foothold in slaver's bay.
The way she is going - she will have an unfortunate incident happened to her pretty soon in the story
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.
Littlefinger:
He has an enormous intellect, exceptionally so. He is likely quite rich by now, I would assume he managed to divert a great hoard into the bank accounts of free cities. He has a lot of friends everywhere, and he has no sworn enemies whatsoever. He is very likely to be one of the few victors of the series. Smart political moves, careful diplomacy and swift management of threats is his "plot armor". Also he is not really at odds with Varys. Their "rivalry" only for the show. I will not be shocked to know that they are a part of the same conspiracy.
Varys:
He has an immense amount of money in his disposal(both from essos friend and westeros lords), as well as knowledge in the espionage. Having the greatest spy network and faking complete neutrality/loyalty he is pretty much out of scope of anyone who would like to and had means to discredit/plot against someone. He, like Petyr, has no enemies until late, and now his enemies are on the brink of destruction (because of enormous amounts of errors they have made. Those errors are on-par with Stark errors, but were done in a shorter period of time.)
I am pretty sure his network works pretty much like modern spy networks, where every bit of information is verified by several channels. Also his position gives him an advantage of actually participating in everything that is going on as a double agent, brokering information for both sides in every conflict.
Freys(as well as Boltons):
Dishonorable or not, but they are quite vulnerable right now. They will have to either rule harshly or perish quickly. In either way Red Wedding will haunt them for quite some time. But Freys are still in better position, for not having an army freezing at their gates.
Edit:
Oh, forgot Jaime.
He is honorable alright. He was honorable all along. He killed his king, but the king was mad and wanted to die anyway, along with whole city. He loves his sister, but such is love. You cannot blame a man for falling in love. He threw Bran out of the window. Wouldn't you do the same to protect your own children? He was honorable all along, but latest events made him think of how he is perceived by others, and he was forced to work on his image.
The only reason his reputation is so tarnished is because he is associated with Lannister family, and at least two mad kings(I would say three, but honestly Robert was more incompetent then outright mad.)