I would guess one of the reasons Joes are so well done is:
1 - It is the company brand and
2 - They aren't paying royalties on them - which keeps costs down (although reports are coming in that prices are going back up).
1. Absolutely true. However Marvel as a company should demand the same quality as Hasbro is still making the lions share of profit on MU figures. Also as Marvel is now owned by Disney who tends to use Mattel as their toy manufacturer it would behoove Hasbro to up the quality, so Mattel does not under-bid them on the next go around. We would then be stuck with craptastic MU figures.
2. I am still willing to bet they are not anywhere near losing money on these fellas.
Plus I am still waiting for (and will obviously be waiting a long time) for a nice Marvel/GI Joe crossover or at the very least like a DC style elseworlds where Joe and SHIELD are linked and such. I like the idea of SnakeEyes training with/ Cap and Black Widow. Or something along those lines.
Batman would be a great Joe crossover as well.
Or Zartan Sniping superman with a Kryptonite bullet. (This was mostly made in jest I know it would not work.)