The biggest thing of all, is that Shadow Dragon is just a remake, it isn't a new game and thus shouldn't increment the numbering.
I will get this point out of the way ASAP: FE3 is called FE3 because it is an entirely new game with an OPTIONAL remake added in. That's why it gets a new number.
It would make far more sense for remakes to share the same number of the game they are a remake of, and include the platform the remake is on. So, Shadow Dragon SHOULD be either FEDS, or FE1DS, not FE11. If, for example, FE4 was remade on the Wii, we would call it FE4Wii, rather than say FE13. It is undeniably clear that FE4Wii means a remake of FE4 on the Wii, and we wouldn't have to be TOLD that it is that, whereas calling it FE13 means we would have to know for a fact that FE13 is a remake of FE4, and the numbering just starts getting more confusing.
It is just a far simpler system that makes loads more sense.
Would you rather have it like this?
FE11 - remake of FE1
FE12 - new FE
FE13 - FE4 remake
FE14 - new FE
FE15 - new FE
FE16 - Remake of FE5
FE17 - new FE
FE18 - Remake of FE7
Or, like this?
FE1DS
FE11
FE12
FE3DS
FE4Wii
FE13
FE5Wii
FE6Wii
The latter is far easier to understand
But really, using a number system is pretty bogus in the first place, just use acronyms, this isn't Final Fantasy! They're far easier to understand than numbers, because it's super easy to tell that FE:SnK means Seisen no Keifu, and you don't need people to tell you "lolno, FE4 isn't Thracia 776, it's Seisen no Keifu, you noob".