4e's Saves as Defenses originally came from Star Wars Saga Edition. So that's probably the game to look at on how/why WotC really changed how saves would work.
The original idea for why Saving Throws came about is because Gygax and Arneson saw them as another chance for the characters to Survive. To them, only heroic characters had saving throws because saving throws let these PCs survive against supernatural forces, special abilities, and things that are magical where a normal, non-class character couldn't.
That's why the Saves were against things like Magic, Dragon Breath, Wands, Petrification, and so on. These are all non-normal and very much supernatural in origin.
When WotC changed them to Fortitude, Reflex and Will, they lost their significance. Now ANYBODY could try and Save. It was no longer special to just PCs. PCs lost a bit of their heroism.