Now, it will be interesting to understand the reasons of this performance. Is it because SQEX was not able to deliver the message, that is the game was worth playing for all who enjoyed the original entry? Is it because 3DS' fatigue? Well, perhaps yes and no; it seems Fire Emblem If is getting a lot of preorders and if that game is going to sell more than Awakening, it will likely be the first reason (Fire Emblem If is more differentiated with respect to the predecessor).
I think its safer to say, given what Nirolak posted above, that its the former. Not much reason to have faith in the sequel if SQEX itself didn't seem to care about it.
Yeah I don't think "3DS fatigue" is really a thing in the same sense it would be after a new system had come out.
The biggest issue for new games currently is:
1.) There's a huge catalog of titles people can buy for cheap (either new or used, varying by title), so there's less incentive to buy a new game unless you play through tons and tons of games on a regular basis.
2.) The system is kind of old now so it's hard to give people the impression of freshness or garner heavy interest on an audio-visual basis.
3.) There's still a lot of games coming out at a fairly regular pace, so beyond the catalog, you have a fairly large amount of upcoming titles you can wait and buy instead while you play your old games (or even games on other systems since there are a lot of releases right now).
The benefit is that there's a huge install base out there, but that's only helpful if you're a notably exciting title. This is generally the basis of market polarization, since a lot of people have the system, but they're all pickier about what they're buying.
Bravely Second came off as a half assed sequel. Fire Emblem If on the other hand, even though we haven't seen a lot, is being presented as a major title that's important to its publisher. It's getting two editions. There's a big special edition and major DLC announced. The production values look good and the content all looks new. They point out the game is three times as large as Awakening if you buy all three campaigns. There's a tie-in card game. There's was a high effort Wii U spin-off game that was announced at the same time. For the more core fans they announced some mechanics changes that could notably switch things up.
If you look at the game you get a sense of importance, the feeling that this is a large title, and that the publisher really cares in a way that never came across with Bravely Second in comparison. It's the kind of title I could actually see benefiting from the late cycle market conditions. Now, I need to see a bit more to really get a sense of it, but the initial showing is promising and I think you see pre-orders reflecting that.