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Joel is waaay superior to Mike (and I say that being a big fan of Mike, including his post-MST work). It's sort of an even dorkier arguement than Kirk vs Picard. I think Joel, much like Kirk, appeals to the goofier (and often more stoned) fans, whereas Mike is a little more sophisticated and smooth.
Really for me the turning point of the show was the loss of TVs Frank. He was the heart and hair of the show. Once he was gone it just wasn't the same.
*hike, hike, hike your pants up, hike hike with... the thing... and... the..... football.....*
As I huge fan of MST, which I discovered I think in its second season on the Comedy Channel and as someone who loves Joel's work, I really think that Mike is just a bit better at it. There was a reason they put him in as head writer. Too me the essence of MST and why I love RiffTrax so much, is that it replicated an activity I was already doing: namely hanging around with friends watching cheesy movies and making fun of them. Joel, whom let me reiterate I think is great and have no issues at all watching his episodes, but doesn't quite strike the right tone for me - too much prop comic (which as this post attests is his roots) with things like the invention exchange and his more paternalistic attitude with the bots. The heart and soul of it all was the movie riffing and for me personally I really enjoy Mike, BIll Corbett and Kevin Murphy the best for that.
(and yeah, Mike is in the hollywood Libertarian camp I think. But he's a comedian first and foremost - there's about as many jokes about conservatives as liberals in Rifftrax, though both are a minor topic matter in their riffing)
Oh I should also add I spent most of last weekend watching the Mystery Science Theater 3000 20th Anniversary set which Shout! Factory just put out. Fantastic set and definitely worth getting for the MST fan. There is a decent documentary broken into three half hour chunks, four previously unreleased MSTies (one Joel, three Mikes - sorry Joel fanbois), the Comic Con panel with all of the cask members all in a nice metal tin with a Crow figurine.