There were non-weapon proficiencies long before the Skills & powers book, if I remember correctly it was roll under the relevant ability score.Before 3e there were very few rules around adjudicating success or failure of skills, at least not until the Skills and Powers book came out. For the most part it was just up to the group to figure it out. For better or worse there's significantly more rules on how to resolve the challenges. I think it's for the better but older editions still have fans. So for me getting rid of that system bonuses and penalties altogether (instead of just replacing them with something roughly equivalent) would be a mistake.
But anyways the point is more that you can make ability scores mean less while it still being and feeling like D&D.

