I'm converting my ongoing party of 15th level adventures from 3.5 to Pathfinder in a couple weeks, and I'm going to be implementing the Inherent Bonus system from 4e.
I'm keeping exactly the same rules as Pathfinder (+1 to AC and saving throws at levels 4, 9, 14, 19 and 24; +1 to attack rolls and damage at levels 7, 12, 17, 22 and 27). We'll see how it goes.
I'm ruling that the bonuses to attack, damage and AC are enhancement bonuses, the bonuses to saving throws are resistance bonuses. This way they will overlap with the bonuses provided by some magic items - although not all magic items. There will still be things out there that can give players an edge.
You can still have magic items in this system. A 17th level character has a +3 inherent bonuses to attack and damage. If that character picks up a +5 sword, then they still enjoy the benefit of the magic item (a +2 net gain in this case).
The rate a which these inherent bonuses accrue is probably slightly behind the power curve as far as magic items are concerned. So the rules don't replace magic items, but they do shore up the deficiency in those who don't have them. And of course, these inherent bonuses are not magical... so enchanted weapons would still be needed when facing anything with DR/magic.
I agree that this is a play-style thing. I'm not adopting these rules because I have a lot of combat (quite the contrary) but because I don't give away treasure at anything like the rate suggested in the rules. I recognise that the PCs need these bonuses to punch their weight in the game, but I'm unwilling to fill this gap with magic items.
I prefer magic items to be rich and storied creations. I just don't want to be bothered with having to remember that I need to upgrade Bob the Thief's armour from +2 to +3 just because he's turned 14th level.