The last time I had a subscription to Archie-Sonic was in the mid-'00s, so I was used to seeing Mobians drawn with more humanoid proportions (though IIRC I was still confused by things like the Archie/SatAM crew having visible necks and the SEGA guys lacking them, and the differences in hand sizes/number of fingers). It doesn't bother me, and eventually that's how my style developed, albeit I do try to keep their overall proportions different from humans'.
You know what DOES bother me? Failure to adapt humanoid features onto an otherwise strictly SEGA-esque body, either via weirdly-shaped bodies (that circle-pelvis thing Archie used to have going on with some of the girls, like Julie-su) or by stretching them into noodle Mobians (often a result of trying to give them more humanoid proportions but refusing to ditch the noodle limbs).
There's also plain old style dissonance (ex: one Mobian has human-ish anatomy, another Mobian standing right next to them has garden hoses for arms), which brings me to another topic:
One of the most common complaints about 06 is that every single human in it is firmly lodged in the depths of the Uncanny Valley, in part because they interact with characters modeled after Felix the Cat (the humans in 06 are meant to be semi-realistic). This got me wondering a while back: would humanoid anatomy on Mobians make it easier for them to comfortably co-exist with humans and humanoids who aren't as heavily-stylized as the ones in Unleashed? (Shahra and Merlina would be a good in-between point of reference, I think) If you're not careful it can still end up looking awkward, but at least there's some common ground between the two groups, if that makes any sense.
(Granted, 06's Mobians were affected by the Valley in ways that didn't require human involvement, mostly because none of the in-game models could properly emote, yet they were capable of some subtle, semi-realistic bodily movements. It did seem to work with Mephiles, at least)