For me, the Epilogue totally redeemed the atmosphere of the Witcher 2 in my eyes. Don't get me wrong, it's doubtlessly one of the best RPG's to hit the PC, but throughout the game I kept comparing it to its predecessor. And I just felt more emotionally connected with the first game. However, the Epilogue simply put the ending of the first Witcher to shame, it was a perfect example of why every story shouldn't end with the big, bad fight between the good guy and the bad guy. Quite simply because there is rarely a "good" or "bad" person, just people with their own grey characters, sometimes swaying towards the light, other times - to the dark.
When Letho told me his story, I couldn't help but tell myself: "He's in this because of ME". Think about it, if he and his company had just left Yennefer behind - they had no reason or obligation to look after her - they would never have been captured. They would never have been sent to the Northern Kingdoms. His willingness to look after her proves that Letho is, in his way, a man of his word. He owed Geralt his life and he repaid him, even when Geralt was no longer in a position to force him to return the favour.
Even after that, when he fought with Geralt and decided to spare his life. Letho said he owed him, but did he really? He had already done his part by looking after Yennefer as long as he could, in the first place. And yet, he left Geralt live. Finally, if you chose that path of course, he ends up saving Triss. Why? What more does he owe to Geralt? He already looked after one sorceress, spared the Witcher's life and now saved another of his lovers. To me, this is an obvious indicator that the man is not completely lost. Yes, he did a lot of harm - he killed a lot of people, but if you look at it that way - did Geralt not do the same?
Because we play as Geralt, he is the main character in this story, it is only human nature to sympathise with him more. We associate with him and we assume that his way is the right way. And yet, when we look at it - the Outskirts of Vizima, the assault of the La Valette castle, the pogrom in Flotsam (which is one possible outcome, but still), the the battle of Vergen (if the mist had just stayed there Henselt would have no choice but to turn back) and, in the end, Loc Muinne. Some of this is not directly connected to his actions, but Geralt's overall meddling did stir up a lot of problems. In a way, depending on the player's actions, he could potentially cause just as much harm as Letho did.
And let's not forget the motive. Letho didn't do this for gold or glory, or some other such. He did it for his School and, ultimately, that is what moved me. Witchers are a dying breed, if one is trying to restore a part of what was lost, who am I to get in his way? More so, with so few of them left, isn't it criminal for them to murder each other? For no particular reason, aside from the fact that they got caught in the major powers' political ploys?
When you think about it, Letho and Geralt are not that different. They are social outcasts, rejected by society for whom they are. And each of them is trying to make his own way in the world, doing this that may not always be classed as good or honourable. In the end, both are trying to make the two ends meet, using their unique skillset; only when politics enter the mix do they fuck things up as usual.