Layering your story with strategy

Not really having a theme this week has thrown me off a bit... I mean, the possibilities are endless to talk about! Haha well, I have recently been watching a couple tv shows that have just really made me appreciate the talented gift of writers. We really have the ability to transform a simple story into something epic and profound, and give to give it meaning and depth. I have found that the most enticing stories have phenomenal interwoven story lines and plots that have been well thought out and strategized. Homeland or Breaking Bad(these are the shows, by the way), two wonderful examples of plot layering. I realize these are both tv shows and not novels, but I am mostly concerned with the writing and structure of the plot. I don't plan to spoil any of them for those that haven't watched them, but those who have seen them can maybe understand what I mean about the layering. Every plot twist seems to make sense, and even if it is a little out there, you have to make sure your characters motives and goals are intact with the plot twists. They have these imperfect characters and they either grow as the plot thickens, or they deteriorate, but they never stay the same, they are always having to change, and adapt.
Breaking Bad's overarching theme is watching this normal man become an anti-hero. With every twist, and with every turn, we watch him sink lower, and lower, but yet we still cheer him on. The choices he makes are very decided and he knows what he wants as a character, albeit his motives are skewed.
Homeland's intelligent writing and characters are what make this story a success. Again, the characters are deeply flawed and when they make mistakes, they are mistakes that affect not just themselves, but the Nation. Every move is calculated and thought out, and its hard to stay ahead of the bad guys.
I think the things that intrigue me the most about these two story lines, is that it puts into question our humanity. They ask questions, or put the characters through situations that I find myself saying, "How would I respond?" or "What would I do?" They are stories that make you want to evaluate yourself. That is what I consider good writing, when you can tell a story, but also make the reader (or consumer) turn inwardly to connect with the story.