Really equal.
However, if pressed, I vote Mike. Still, both Joel and Mike are awesome.
Mike. Joel seems so sleepy he makes me tired. Maybe he could run for president.
This. I did like how Joel was like a parent to the bots but Mike was like a big brother. Very different styles, but both funny as hell.
I never liked Mike’s style.
I agree with the assessment that the show became more acerbic after Joel left which I enjoyed.
I also think Mike was cuter which I know is not really a valid reason, since most of the time all we see is the back of their heads but so sue me, I’m human.
I like 'em both and didn’t really have a preference.
However, I definitely preferred the original Mads (Dr. Forrester and TV’s Frank) to Pearl.
I was surprised not to see “Joike” as a possible response. Then again, I can see if the OP really wanted to make us actually decide.
ORIGINAL?!?
Fake geek Doper!!! 
I think Mike just edges out in front of Joel for me, mostly because we share a the same moniker. We Mikes got to look out for one another.
I gotta go with Mike. Joel was an absurdest comic that I didn’t like very much before the show. Am I the only one who remembers him on SNL? That humor carried over to his inventions and the pieces between movie clips. I thought those parts fell flat most of the time except when Mike was involved. His movie commentary was fine and I still loved the show then but I thought the Mike episodes were funnier.
Joel may have another chance at it.
I remember Joel from SNL. He did a routine with a Mr. Quarterback, which I thought was hilarious partly because I owned a Mr. Quarterback. (I was probably 10, 11 at the time.)
I always found his standup to be too Kaufmanesque although he just had the one sleepy persona instead of a bunch of characters.
Not that I disliked him on MST3K. Just the opposite. I feel in love with the show with Joel. I just thought the shows with Mike improved and they aged better.
Bonus: Joel talking to Seinfeld in Comedians in Cars.
At one point I would have been very strongly on Team Joel, but while I still lean in that direction over time I did come to appreciate Mike and his own hosting style more.
A friend once mentioned that while he liked Joel a lot he felt the parental relationship he had with the bots by its nature wasn’t as funny as the more equal relationship Mike had with the bots. I hadn’t thought about it that way before, but this may also explain some of the more acerbic humor in the Mike episodes. A joke involving the characters making fun of each other might come across as mean-spirited if the audience perceives them as a father and his children but be fine if they’re perceived as having a sibling-like relationship.
Joel.
Mike was no slouch, but I liked how Joel’s sense of humor was sweet and non-ascerbic and sleepy/dopey/bashful[del]/and Doc[/del]. It made him stand out from the usual biting-and-sarcastic crowd.
“You wake and bake!”
I voted for Joel. He seemed to fit naturally with the Bots. Mike had more of an edge.
But, heck, I’m looking forward to the next round of MST3Ks, too.
Mike! Both are, of course, great. Joel always seemed mildly stoned, though many times to good comedic effect.
That’d just be mean - Tom’s self esteem would take a hit when the results come in for Croooow.
My preference for Joel was justified when I learned that Mike is a right-wing religious Republican.
There is the Mike of real life, and there is the Mike of the SoL. They are two distinct individuals.
(Although, yeah, the needle just swung a little towards Joel for me, too.)
I understand the appeal of Joel and he was first, but I find Mike a lot funnier.
I love them both, but I like Mike. I thought Mike was a better foil for the Mads, even though Trace Beaulieu - oh man, I spelled it right on the first try! - bailed on the show early. I really liked the Mike Nelson, Destroyer of Worlds sequence.
I know this is blasphemous, but Pearl kind of edges out Dr. Forrester and Frank for me (and I’ve never seen whatsisname…WAY before I ever heard of the show).