It's been brought up that Transformer toys are harder to develop and produce than MOTUC toys and I agree since MOTUC reuses a lot of parts which a transformer cannot.
How about them using a Collector site to release more 'premium' versions of their retail figures? With better paint apps and perhaps new G1 inspired accessories or parts such as a new more fan friendly head in a similar form that Botcon does. This would also include reissues and proper Hasbro releases of the Japanese collector lines such as Alternity.
In regards to FunPub, they would still have exclusive rights to their own toys since they are very 'theme' based anyways and I seriously doubt a Hasbro collector website would compete with them as long as they are not producing the same figures. I find this comparison irrelevant specially when FunPub exclusives are not exactly accessible to everyone.
A Hasbro collector focused website and lines could even take the wind out of the 3rd parties if Hasbro begins to sell upgrades and accessories with perhaps the odd completely new fan requested figure which Walmart would have never accepted.
MOTUC figures sell for US$20 and although this is typically double the price for an equivalent US retail figure, they still sell out within the hour! Some of the larger toys that cost $30-$40 still sell out within the same day! Imagine a Transformer figure with arguably double the budget to produce.
I think that at the end of the day, Hasbro has no will to do it so it's not so much that they can't but more that they won't.