The major thing to keep in mind when watching R&M is that it's very evident they are trying to find their correct niche', and trying different stuff.
because of that you will get many differring opinions on it.
Personally, i like that they've been trying different shit. you can even see them progressively moving from story-driven continuation to simpsons/futurama style "anything goes every episode" type stuff. Not sure if it'll end up at one or another, or remain an amalgamation of the both.
Towards the end of season one, things became a bit too serious. even though the story was pretty neat, having to allocate time to the story means the comedy of the episode kind of depreciates.
My two cents, anyway. Harmon's writing is always very exploratorive.