I meant, does having to carry so much of the story damage their plausibility or character development
OK. In the short run I would say no, since more screentime allows more opportunities for character development. Plausibility is an especially tricky thing on a fantasy show like this, which does ten impossible things before breakfast. I know for me, with this kind of show I often reach a point where so many implausibilities have piled up that I can't suspend disbelief any more. The characters who get more screentime could get there sooner, I guess. It's hard to say at this point.
do the mechanisms used to keep them front and centre inadvertently damage the character
I think it's more that it damages the story than the character, but it's fine line.
I definitely think that the screentime in bad stories is hurting some of the male characters.
We really didn't need to see Sylar until Maya and Alejandro turn him over. Actually he would have been ten times better if he just showed up with surgery scars calling himself Gabriel Grey in the middle of a mexican dessert. but the boat has sailed on that one.
Very true, but this is a general problem with season two IMHO. We also didn't need to see Maya accidentally unleash her power three times, we didn't quite so many scenes at Claire's high school, etc.
One thing I do like about the male characters is the vulnerabilities they're given. In particular I like how Peter and Hiro go against manly-man comic book stereotypes. Peter's emotions are central to his powers and story, he's a nurse, and he was central to the first season without being all noble (I also find him one of the less admirable main characters, but that's a whole other post.) And Hiro of course is all cute and silly.