There's also a lot of bookkeeping that I'm not crazy about. For example, any armored hit location that is damaged fails to provide protection for the remainder of the encounter. This can be a real head ache for the Ref if he's got several wounded NPC's--having to keep up with who got hit where. And, players will have to record or remember where they where hit in previous rounds if hit a second or third time.
That's an excellent point. Having a modified character sheet to deal with this would be useful. If not collected on the char sheet, then a separate PCS sheet for PCs and NPCs to track all the penetrations and damages would be a real benefit.
Though of course, we don't have to use the location component of the PCS, though it does add nice detail.