[Suzerain of Sheol]

Well, it's hard to discuss without spoiling, so it might be better to wait until you finish watching the series to delve into it like that. This really isn't a series you want to get spoiled.

To address some of the things, you said, though, I thought the Eyrie (Lysa Arryn's castle) was kind of unrealistic, both for the fact that it would be nearly impossible to build, and the fact that it's strategic value would be rather questionable, given that there's no possible way it could be self-sufficient, and if the Vale was taken, all its impressive defenses would be meaningless, since the castle would be starved out very quickly.

And they actually adapted the books very well. They only really cut out little things that you don't really miss, and they added a whole lot of scenes that really flesh out the characters and fit perfectly into the storyline.

As for your other point, I won't say too much, but I'll just note: it's more complicated than you think. No matter what, it's more complicated than you think. :p

The details of Jon Arryn's death don't get fully revealed until much later in the series. It's a mystery that keeps building all throughout the story. What you have so far is only a piece of the puzzle.