Um...Being in Amestris isn't what MAKES Edward an Alchemist necessarily, and regardless the character is still from his own setting anyways with actual reasons as to both why he's now on our Earth and as to why his Alchemy still works, or at least he's supposed to. If nothing else Alchemy can be considered a type of magic, which exists in our fused DC/Marvel universe already.

In the case of John Carter the ONLY reason he has any powers is because Mars has a different, lighter gravity field than Earth. He doesn't have any powers or a magic system or anything like Ed has. Carter's powers are completely circumstantial, and any human from Earth put on Edgar Rice Burroughs' Mars would have them. Putting him on Earth and still having him keep those powers makes absolutely no sense unless you change him to the point where he's John Carter in name only.

It's like saying Superman should still have all of his powers while living on a planet with a red sun. You could maybe do it (and considering the long run history I'm sure someone has done it for Superman) but it goes against the nature of the character and their powers.

This is all for the GM to decide anyways, but the comparison to Ed isn't very valid.