As a collector and seller of these things: limited, collector, special, etc... I say that the GS version will be heads and shoulders worth more and you could make a nice penny if you keep yours unopened and would be worth your time, especially if you can lock this in on some upcoming deal? Now this is just my hunch and speculation as I am pretty good when it comes to things like this.
Normally GS does not like to keep huge overhead of these bigger collector’s editions due to storage space concerns especially when so many games and versions will be coming up during the holiday season in rapid succession (Star Wars Force Unleashed 2, LBP2, Gran Turismo 5, Dead Rising 2, the Guitar/BAND games, etc...). With that in mind, they will end up having a much shorter cut-off date for preordering this unlike the other version which will be everywhere.
Furthermore, this is a true GS rarity as far as CE are concerned as 99% of the time the bonus is only different DLC or some cheap swag thrown in outside of the game itself. The last time I remember anything exceptionally different and exclusive for a GS CE was the Red Dead Redemption CE which nobody else had. Even then, that had just some DLC and a soundtrack which were put inside the game case with a different cover sleeve.
The last time GS offered a figure that other stores did not do was Dante from Dante's Inferno and that was just the NECA toy in a plastic bag. To actually have a totally different physical item like this packaged inside the CE seldom happens. Since the other version will be flooded to every merchant and probably on UBI’s website, you can easily pick one up on launch day or just wait for the inevitable UBI 50% price drop in a couple of months. They will have so many of these other versions that it will drive up the price of the less made GS version.
Either they will buy the JITB by itself for a decent price like $40-50 (trust me, people were paying more than the cost of the game for the Amazon DLC for Transformers WFC and Mod Nation Racers) or want to pay over market value for an unopened CE for true fans of AC that are here or international. I already have some of my international friends asking me to specifically get them the GS CE version and want to get me the Codex Edition in return. I could be wrong, but doubt it as GS will not have an infinite supply of these items as UBI is making this just for them and usually once an item has been exhausted by GS, they seldom get restocked and if they do it is first come first serve.
I hope this helps some of you out?