Both the change from Proficiencies to skills, and the changes in saves, are a big deal that I don't see people often recognizing: they shifted shifted the burden of success away from the PC to the world. That is, when you have roll under stat proficiencies, or roll over this (admittedly arbitrary) category value, those DCs are internal to the character and a measure of their inherent competence. When you shift to a roll plus modifier vs a DC, the importance of the character's competence is lessened and potentially even nearly eliminated when you have weirdly high DCs for stuff. In pre-d20 versions, you made a save versus dragon breath because YOU were that awesome. In 3E you failed because the dragon was that awesome. That is a meaningful change.