I think a mechanic that only allows the Agent to slot 3 specific inventory items to bring into PvP to use would work. Of course, limiting the items that can be used or limiting each item to 1 per use would have to be done to avoid the (un)hilarity in PvPs infancy.
The advantage of the Agent is his use of top secret weaponry, high-tech uniforms, and his cache of items to aide the battle. It's understandable why PD took it away (First turn Cap + Chrono Accelorator(s) + OTK setup = GG), but always hoped they returned it back in a milder format.
I think that would be a waste. Allowing infinite use of items would make Researching, and the store more valuable, but still being annoying to implement. Seriously they haven't even given us alt layouts for the agent yet.
Civilized men are more discourteous than savages they can be impolite without having their skulls split. Official Phantom Stranger of the C&GN
All you'd find in PvP are Cripplers and stuff. No thanks. :P
Which is why the option for certain items to be used (store bought items, Research Only items, or flavor of the month items [Lost Pages, Munitions, Easter Eggs, etc.]). We're trying to avoid the Cripplers, Chronos, Elixers and the like because they do cause loops that kill the game.