Great question. I don't know the specifics of the CRAP coin system but based on my digging around in the 2das, reading the CRAP installation guide, and checking out their scripts:
Pro:
(1) This system can be used without CEP and is very lightweight.
(2) PnP Coins removes the weight from coins which means that builders have the option of encumbrance (or to not use it like default gold) and handles weight via script which allows for the correct 3e 50 coins = 1lb ratio (which could be altered within the script to be more or less according to preference).
(3) PnP Coins can handle multiple types of currency in the same module out of the box. In other words, Silverymoon could use one set of coins while Cormyr could use another entirely (see the FR 3e campaign setting book to see what I mean). You could tag them and resref them to where they are interchangeable, or create moneychanger NPCs to handle it (with a fee, of course).
(4) PnP Coins has a 50,000 stacking limit on coins rather than 100, making organization much easier. It also does not require a coin bag. I believe that having a higher stack size reduces the strain of creating a lot of coins (in a chest, suppose) because in PnP Coins, if you create 100,000 coins in a dragon's hoard, you have only created two stacks of items, whereas in CRAP you have created 1,000.
(5) From what I have seen, my system handles the coin variables more efficiently by having several if else statements per coin per function measuring coins up to 10,000 at a time, reducing CPU load especially where lots of coins are concerned.
(6) Variables are only stored temporarily as the PC talks to a merchant rather than on items or oPC. All the values are saved/loaded by reading the tags and resrefs of the coins when the PC opens a store.
CONS:
(1) PnP Coins does not yet automatically handle treasure generation like CRAP coins do. Builders will have to slightly alter their treasure scripts. Not terribly difficult but something I have not gotten around to yet. Just like CRAP, if a builder uses a custom script already, he or she will have to account for the new coins in that script.
(2) I'm sure there is something else, I was just comparing our features list.
Due to the fact that I based a lot of my work off Accerak's PnP Coins for NWN2, and he was a CRAP member iirc, my system takes all the functionality of CRAP (besides the treasure generation) and makes it more efficient and adds a few features on.