The way I see it, a chain is only as strong as its weakest link.
So if one of the main factors - rider/bike/team - is somewhat lacking, then that's the deciding factor.
Put me on a GP grid with a Repsol 'onda and I'd come last, because I'm crap. Put rossi on my DD bike on a GP grid and (maybe!) he'd come last.
I'd suggest it's coincidence if there's different bikes dominating different series.