I think I'm the exact opposite of Sprocket.
I watched everything in a couple of big lumps and I wasn't really into it until the last couple episodes of season one (which kind of kick off the plot-crazy of season two). I found season three awesome but I have to go back and pause and see what they're referring to and be all involved and stuff. I think the episode 10 you're referring to is Lepidopterists which I thought was really funny, and the stuff I find 'eh' correlates with a lack of Doc Hammer's involvement.
Lepidopterists was my absolute favorite episode of season 3, hands down. Everything just came together for an episode that worked so well. The monarch moves further into a dynamic character, the OSI is fleshed out a bit more, there's finally some elaboration to the seemingly pointless competition between hero and villain, and Mr. Doe and Mr. Cardholder just fucking rock.
I feel like I have to watch ORB again though. I came off at first a little unfazed, but there's a lot of glowing things being said about it so I probably missed something.
and @ Dean's "heart problem", I think that's there to draw a parallel between the two boys. Hank's being sucked into the insanity of the world around him, as Dean is being pushed to the level of our world. He's still having trouble digesting the idea of the clones, and also has been pretty removed from most people. He didn't get the time with Brock or Brock's son (?) that Hank got. I want Trianna and Orpheus to come back to see this go somewhere.