Eh, I was fine with the lack of a single over arcing plot for the season. The episodic stuff mostly worked, though there were lots of missteps everywhere. I tended to like it more than Season 2 overall (just barely) if only because I thought the whole plot line with V overstayed its welcome and ended on a ridiculous slapstick note. It was a well deserved comeuppance, but it felt like a really rushed conclusion.
I find myself really liking Caputo despite myself. He's somehow been elevated above being just a sleezeball to being a sleezeball who's actually trying to do good and right by everyone while being stuck in impossible situations. The fact that the prison is a circus of one disaster after another (Seriously, tabulate the amount of shit that's gone down in the space of, what, less than a year? How many escapes alone have they had? I can't imagine this would be normal or realistic, but I've never been to prison...) just makes me feel bad for him.