My issue with the Mii Fighters is that they're boring. The three archetypes don't really have much to offer that other characters within the archetype don't already have (for example, why play a generic swordfighter when we have Link, Shulk, Cloud, the entire cast of Fire Emblem, and more). Even the one that stands out the most is just Samus with a twist. Even ignoring the fact that they very closely stick to incredibly well populated archetypes within Super Smash Bros., their Special Moves are almost entirely just generic versions of of other characters's attacks (for example, instead of allowing people the fantasy of being able to do a Falcon Punch, they get a generic version of the move called Exploding Side Kick). The ones that aren't like that aren't really all that interesting from a visual/conceptual standpoint like Shot Put.
The other issue is that they really are "almost not even Miis anymore". Miis may be avatars, but they're not without their personality. They're silly and goofy and always up to wacky hijinks. In Super Smash Bros. the Mii Fighters are uncharacteristically serious, and it strips away all of their charm. Combine this with the previous issue, and the appeal of the Miis are strictly for the novelty of a character that can be anyone.
I think the Mii Fighters at least need a face lift. They need to get back that charm that they have in other games, and the archetypes need to bring things to the table that aren't just mildly interesting at best.