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.
Hard to say really though.