I'm thinking of doing the same thing for a campaign I'm going to start next month. I decided that all shields were actually a form of Cover. A large shield provides half cover (+4 AC, +2 to Reflex saves), a small shield provides one-quarter cover (+2 AC, +1 Reflex) and I made Bucklers be "1/8"th cover (+1 AC, +0 reflex). These bonuses are Cover bonuses and therefore won't stack with Shield or other Cover bonuses.
I haven't implemented this yet, and I'm actually going to let my group vote on whether they want to use it or not. I did this because I'm bothered by the fact that Shield bonuses only stack with mundane Armor bonuses (enhanced or otherwise) but not with Mage Armor or other similar things (Inertial Armor, etc.). Since you aren't Invulnerable if you have Mage Armor up, and someone can still hit you, shouldn't your shield still provide some defense once they get through your Mage Armor? And if you feel Mage Armor surrounds you and not your shield, shouldn't your shield have a chance to block something before it gets to your Mage Armor?
I thought about just giving Shields a Shield Bonus rather than a Cover bonus, but I like the Reflex aspect and this uses an in-game mechanic which I like.
Thanks.