It's actually intra-party stuff that bothers me. Say a character has a skill in navigation (navigator's tools). In general he's only slightly more likely to be successful navigating than any other character. And a wizard will generally be better than the "professional sailor" unless that sailor has a remarkably high Int. It underplays the importance having trained vs. raw ability IMO. An extra +2 bonus (or so) might work, but in general I just won't let someone without proficiency do certain things (admittedly usually only if one of the other PCs is proficient, but still...)
Edit: and for the record, I really like bounded accuracy in the context of combat (other than wanting a tweek to saves).