When it comes to comics, no matter how well you sell, or what licences you own, if you are not Marvel or DC you are Indy. That is the best way to explain it, The Walking Dead has outsold everything, but its an Image book.
Marvel had some really good storylines in the 90's, with Maximum Carnage, Age of Apocalypse/Legion Quest, and Onslaught, and admittedly I was more of a Marvel Zombie back in those days(I only bought Marvel books, and Spawn, because McFarlane was my favorite Spidey artist), around the time the Onslaught story ended was when I stopped reading until I found out about The Walking Dead(issue #48). I only recently started reading DC stories, starting with Crisis on Infinate Earths, Infinate Crisis, & Final Crisis, then moving on to the Batman: Black Hand through Batman: Battle for the Cowl, which got me reading Blackest Night. Thanks to my comic shop selling used graphics, I have been able to obtain The Dark Knight Returns & Strikes Back, Superman: Red Sons, Batman: Death in the Family, and Death of Superman, I am now looking for Funeral for a Friend.
Night of the Owls is about this secret society called the Court of Owls, that has had roots in Gotham since before Jonah Hex was running around. They resurrect all of their former assassins to attack the most notible names in Gotham(including Victor Friese, who has the luxury of having Jason Todd rescue him). You find out that Haly's Circus was a breeding ground for their assassins, and that Dick Grayson was intended to be a Talon(assassin), that his grandfather was a Talon, and that Bruce Wayne has a brother that is also a Talon. The big payoff was watching Batman suckerpunch Nightwing, and you later found out that was to unlodge something that was put in his tooth by the Court. Capullo's artwork is amazing, but thats the only possitive I found to that story. The Dollmaker was the first arc of Detective Comics in the New52, and in October they debut the new Joker(who has a Leatherface look to him), after Dollmaker removed the Jokers face in Detective #1.
About the Marvel villains, I bet if you found out a bit more about some of the B-Listers, you wouldnt have such a problem. Taskmaster & Arcade are a couple of my personal favorites, Taskmaster simply has an Idetic Memory(he can learn your combat style in seconds just by him fighting you), and Arcade is alot like if you combined Joker & Riddler, and uses games as death traps. Magneto is my favorite former villain, as the sympathy for him was made very clear, but now it seems like he & Xavier will be forced to team up to bring down the Pheonix powered Cyclops(he better hope that this does not induce the resurection of Onslaught), Jack O'Lantern has been overly amuzing in the latest Venom run, and gives Flash Thompson a unique arch-rival. Mr Sinister in Uncanny X-Men has been the best I have ever seen the character. Marvel's biggest problem is that thier best villains would probably never even see a movie, but I could say the same about DC, as Zsasz will probably only ever just be briefly shown in Batman Begins.
The only Transformers book I picked up was The Death of Optimus Prime, and that was because the cover was just a picture of the old metal Optimus toy. Basically Optimus retires, and reverts back to his Dax name. I am pretty sure the story is still running cannon to Generation 1. The story wound up leading into 2 new Transformers books, so I never continued after buying 5 Batman books, 4 X-Men books, and everything else, I just couldnt get into another multi-arch story.