WOW, GI Joe is only sold via their site? How'd I miss that!
What you see in stores now of the 3.75" GI Joe toys is merely stores trying to move the last of the product they have. At some point, whether it be in the fall or for Christmas, Hasbro will be introducing a 6" figure line called "Sigma Six" or something stupid like that. They will essentially "reboot" the line and be able to start off with all new versions of Duke, Snake Eyes, etc...
They announced back at Toy Fair in Feb of this year that the 3.75" and 12" GI Joe lines were effectively cancelled.
After many cries let out by GIJoe collectors, Hasbro decided to change their tune (slightly) and are now going to be offering individually carded 3.75" figures on retro-style cards (the packaging looks A LOT like the packaging from the 80s) and from what I understood they were going to be available only through their toy shop website.
Now I have seen that online retailers like Brians Toys are going to be selling them as well - but I'm not sure if they are just buying from the store applying a mark-up and then reselling them with the intention of being the ONLY game in town after Hasbro's store sells out or if Hasbro is letting some of their smaller customers buy in to the line. The big chains however, will transition to selling the new 6" line instead.
Hope that helps, sorry for being off-topic of SW.