1>5>4>2>6>3
Season 6's first half was really good, but as for the second half, my sister once put it as "The main plot is so uninteresting it feels like the subplot." I couldn't agree with her more. The most interesting things about season 6 were Brother Sam and Deborah coming into her own. Since Brother Sam is no longer with us (*moment of silence*) we're left with Deb, who has, cheese aside, really been a delight to watch the entire season. Unfortunately, everything else is dull, ridiculous, predictable, or a combination of the three. The big reveal this season was something I saw coming early on, and since it happened, the way it's been handled and a lot of Dexter's reactions to it have been pretty lackluster to watch.
Also, Quinn needs to be put on a table and done away with. He was never able to fill Dokes's shoes, and since he and Deb broke up this season, it shows far more than it ever had in the previous seasons.
Season 1 set the tone for a lot of stuff that people have come to know and love about the show. Season 3 is the weakest of the seasons, but not necessarily because I hate it; it's just that it was a level of farfetched that does not mesh well with how pointless the season was in the first place.
Season 4 was top-notch, but its ending (except for a certain tragic and untimely death) was disappointing.
Season 5 was even better (although not necessarily better executed), and proved that the big-bad and the scenario don't always have to be bigger to be better. It was probably the first thoroughly convincing season about Dexter trying to find his place in a world without the things that anchor him to his code. Yes, the relationship with Lumen and the conclusion of that relationship were cheesy as hell, but it's the first season that actually ended with Dexter feeling like there was hope for him. Also, potentially having a sidekick who wouldn't stab him in the back was just morbidly delightful. Their largely comical and absurd first "date" was a stroke of deliciously morbid genius.
Season 2 was solid, but seasons 1, 5, and 4 completely outclass it. The loss of Dokes, knowing what I know now about who replaces him, also hurts that season.
For the longest time, the show's biggest problem has been that its protagonist walks the fine, grey line between the ethical black and white of things, yet the rest of the show's characters and even the writers are quick to take one side or the other. Season 5 was the first real attempt at the exploration of the grey, which is why it's one of my favorites.