I really enjoyed this game, and the ending.
I chose to save Triss, and have mercy on the Dragon/Saskia.
I let Letho walk, and saved Sile and let her teleport away.

I don't understand. The ending left me with more questions than the start of the game. I have no clue what is going on whatsoever.

I really hate the fact that you have 50 unanswered questions given to you at the end, and only like 1 answered throughout the game. I don't even know what happened or is happening now in the universe, because of how confused I am. What do I do?

Ask questions so that the rest of us can fill you in?

Who employed Letho? What was Sile really doing? Yennefer? What's going on in the Empire? I'm just lost as to what is going on in the world. Like who is working with who and who is good and bad? Honestly I'm more lost than the beginning I don't even know where to start in terms of questions.

did you skip all the dialogue with Sile and Letho? they already explained everything!

the only mystery left unanswered is the Wild Hunt and the fate of Yennefer in Nilfgard..

The emperor of Nilfgaard employed Letho, he explains this to you if you chat with him at the end of the game.

Sile is after power, nothing more. She wants to control the kings of the Northern Kingdoms, the king of Aedirn proved too hard to control and she felt he was a bad king so had him eliminated.

Yennefer is in Nilfgaard, again, Letho explains this to you.

As for what's going on with the world, well it is complex, that's for sure, but it basically boils down to various factions vying for power. Which of these factions prevail depends on your choices in the game so it's hard to be more specific than that.

There is no good and bad, that's the entire point. It's all shades of grey.

Did you ask Letho any questions? He answers like... all of those at the end.

MAJOR SPOILERS READ AT YOUR OWN RISK RAWR I'M A LION

I'll break it down for you chronologically. Before the first game, Yennefer was kidnapped by the Wild Hunt and Geralt set off to save her. Eventually he came across Letho and saved his life, and Letho, whose Witcher school specialized in the Wild Hunt, agreed to help him since he knew where they were taking her.

When they finally found Yennefer, Geralt traded himself for her, so Letho took her in. She managed to get the same amnesia as Geralt has dealt with, so she was a pain in the ass. They wandered around until they were picked up in Nilfgaard. Nilfgaard took Yennefer and used some kind of magic to get her to reveal information about the lodge of sorceresses. They then hired Letho to do the things that he did, promising to rebuild the Witcher school he came from.

Letho met and manipulated Sile and the rest of the sorceresses with the intention of framing them for the killings, but then Sile ordered him to kill the king Demavend, so he didn't even have to find a way to frame them. After killing him, he got in with the Scoia'tael, presumably as a part of Sile's plan to lay low for awhile. Instead, Letho convinced Iorveth to help him kill Foltest (and continue his mission as per Nilfgaard's orders). Sile was actually in Flotsam looking for Letho, realizing that she had been used.

EDIT: Basically the whole thing is one huge power grab, everyone trying to frame one another so that they can seize power.