Agreed. I'm onboarding a couple of new players and see the issues again and again. I'm dropping the overall proficiency score as it just confuses things. skills and abilities just take awhile to become secondhand though.
You could consider playing Shadowdark with new players instead. It's much more friendly to new players.
Proficiency scores are HUGE and extremely important, especially for classes like rogue, bard, etc who rely on them so much - especially for non-combat roleplaying ability or reflex actions.