I think it probably comes down to one of the following:
1. He's got less 'design' appeal than other popular characters in the series. Unfortunately, being 'attractive' seems to be a major part of your popularity in this series, unless you're either known for the interesting microgames (9-Volt, 18-Volt), or Wario.
2. His microgames are microphone based, and that mechanic is not particularly popular. Given that the microgames a character hosts have a large effect on their popularity and characters hosting controversial mechanics tend to be villified for it*, that's not worked out well for Mike as a character.
* See Navi, Kaepora Gaebora, Fi, Fluzzard, the giant bosses in Mario & Luigi Dream Team and LOG from Banjo-Kazooie Nuts and Bolts.
This is hilarious and sadly true at the same time. @CM30 makes excellent points I agree with as well, though I’d like to add that aside from Touched and Gold (to a degree) he has very little screen time with story segments. That alone right there will have some people not give the character consideration at all.
I think it's because of the microphone controls. I dunno why, but many people don't seem to enjoy this style of input. (But I definitely do!)
And also, he used to be the only character related to Dr. Crygor before Penny stole the show.