Berin,

In my homebrew ruleset (based on the d20 SRD), all skills and feats are purchased with experience points. Including the three saves. Most of my party pretty much ignored “buying” them until after their first couple of adventures, and a lot of failed saves against rather mundane traps and annoyances. Suffice to say that they’re all including their saves in their “budgets” now.

I love your ideas on Initiative and Reflex. I’ll very likely change my homebrew to emulate your model. (Currently I’m using both DEX and CHA bonuses to mod Initiative. CHA is used to reflect the personal confidence of the character, and a sort of force of will.)

This is why I’ve always favored standardization of feats. If I, as a player, want +X to saves vs bugbear halitosis, I should be able to toolkit the feat, have it approved by the DM, and run with it. And it wouldn’t break anything, because feats all have consistent bonuses.