Gotta go with Joel, simply because I started watching with him just about from the very beginning. I was really, really bummed when he left.
Also, I really disliked a lot of the later host segments with Pearl Forrester and Brain Guy, etc. Which has nothing to do with Mike as a host, of course, but it rubs off, as it were.
I always liked the Joel episodes of MST3K better, but I gotta admit, Mike Nelson is great at riffing stupid 80s/90s/00s movies, something Joel would never go near (and probably shouldn’t either).
I like Joel just fine, but Mike is my guy. Agree that the show was best with Mike, Forrester, and Frank.
And Mike is really cute. 
I chose Joel because he was the host of the first MST3k episodes I watched, back when they used to cut the episodes in half and showed them weekly on ABC. I thought Joel was so cute (is it just me, or did he look hot in the smoking jacket during the host segments of “Agent Double 007”?) I began trading tapes with some folks I met on Usenet, and discovered the Mike episodes. It just wasn’t the same once Dr. Forrester left and Pearl became the villain, though.
Now I like Rifftrax (with Mike, Kevin and Bill), and haven’t had the chance to see Cinematic Titanic (with everybody else). I notice that the two camps of former MST writers don’t get along, and it makes me sad.
I love them both, and it’s really hard to decide, although I’d have to give Mike a slight edge, since I discovered the show while it was on Sci-Fi.
Mike for me. Admittedly, I was first introduced to the show post-Joel, so I may be somewhat biased, but I though Mike was a much better performer than Joel. The show was just more polished, and the dialogue was tighter - I thought Joel had a lot of funny bits, but the good parts just weren’t as dense as they were later. Of course, some of that may well be improvements in writing as well, but it always seemed to me like Joel wasn’t as into the performing aspect as Mike was, and that made a difference.
I started watching MST3K with Joel, so most of my favorite memories of the show are with him (and he’s the one in Santa Claus Conquers the Martians, so he get automatic points for that). But I think Mike is better talent-wise. Joel came up with the concept of the show and Mike made it work. That Mike’s gone on to more success with Rifftrax speaks well of him, too. I love a lot of the Rifftrax, there’s only a few duds in the lot.
My experience/thoughts exactly.
My total MST3K exposure consists of five (+/-) YouTube marathons. I haven’t seen enough to notice any differences.
(Although, let’s see- Pod People was probably my favorite. Was that a Joel one?)
Yes.
Mike has more good episodes, since the show didn’t start to get really good until season 3, but I definitely prefer Joel. I like the more backhanded way Joel makes fun of the movies. Mike is too straightforward.
Also, Joel does a much better job singing the theme song, which I don’t think anyone can dispute.
Joel. After Joel left, there was no more invention exchange. That alone was worth the price of admission. Oh, that and the Creepy Girl song.
Joel.