The reasons may be more because of us than the game. I'm not saying this as "mind over matter" but rather, should I say, the reverse. The subconscious is taking over the conscious.
Before you ask for a tl;dr (and I will try to keep this relatively short) I want to point out that, by the time you find yourself wanting one, you should already realize the point that's being made.
Now then, think about some things. Do you have a backlog of entertainment? Do you pile up browser bookmarks like there's no tommorow? Did you recently buy the HD re-release of a trilogy of games?
You know that you have these for a purpose, but at the same time, you likely aren't getting much use out of them anytime soon.
The last example in particular is relevant. I bought Metal Gear Solid HD Collection (2 games) quite a while ago, and cleared MGS3 throughout several, spread out sessions. As for MGS2? Haven't even started it up.
Now here comes Fire Emblem Fates with two games released at once and one more released shortly thereafter (if you didn't buy the Special Edition.) By the time you're done with one, you probably don't feel particularly enthusiastic to try the next one in line immediately- you just finished a whole game, you want to take a break, and you aren't particularly obligated to do the two other routes, it's not like it ends off at a major cliffhanger and starts where that left off in the other mode. You lose momentum.
For us that have played Fire Emblem games for a while now, building up that momentum even for the first run of the game we choose is relatively difficult. We are already familiar with Fire Emblem games, and we went out to buy another Fire Emblem game. However, the product we ended up getting is not one that operates as Fire Emblem traditionally does.
Think about how you approached Awakening. We already know about skills from previous Fire Emblem games. The pair up system usually doesn't really mean anything but stat boost + double attack + guards, basically becoming a matter of "It makes a unit stronger, that's all I need to know." Reclassing is something many of us got familiar with from the two games before it too. Child system? All you gotta do is grind out supports, yeah? This kind of stuff is all easy to take in. You more or less play the game like you do most other Fire Emblem games, sans gratuitous eugenics planning for pointlessly optimized characters.
Then Fates comes and messes with all the weapons and the pair up system, even making enemies capable of using it. You have to approach it differently even if you play the easiest of the three games (unless you're on like normal mode or something and just go whatever), and to some level, you feel alienated, "Is this how a Fire Emblem game is supposed to be?" is subconsciously thought.
"The hell are these shield icons below the HP bars?"
"FFFFFFFFFFUUUUUU- I didn't realize that Wyvern Lord would bring a Sorcerer with him to tag team on me when one of them was out of range"
"HIT RATES ARE A LIE"
"Oh right, Dragon Veins were a thing"
You went into the game underestimating it, feeling like your familiarity would let you smoothly cruise through the experience, and got overwhelmed instead.
Of course, this doesn't apply to the sorts who have been following game info and asking questions and the like before the game was actually released, but for those who do think they are familiar with a game, there's even less reason to go about reading a bunch of guides and whatnot instead of jumping in when you have the chance. It also doesn't apply as much to those who played one version long before the official English release and stuff, because they don't have a load to look at all at once.
And at worst, when it comes to the story, since it was essentially built up as one story with multiple routes, but was separated through different games, if you don't bother to go through all of them you're left knowing that you have went through the incomplete experience. You may feel that some kind of duty is left unfulfilled, but at the same time, you can't be assed to keep up the pace, because there was a finish line and it feels like you have crossed it (unless you're zac and you haven't even done your first run through yet.) Just like how games that are released within the same week or so have to compete for sales (because a lot of people are only going to buy one and forget the other), the Fire Emblem Fates games are competing with each other for your attention, and when it tries to take too much of your time at once, you feel more drained from obligation rather than being able to take it easy, and being able to take something easy is important when a big task you aren't particularly good at already is placed before you.
tl;dr : "It's too much, I don't want to bother."
In retrospect I think this might not apply to most the members that bother to come here but fuck I wrote it out already anyway so I might as well post it. I think it's just a reaction to kirant mentioning that Fates seems to be a game that didn't bring much to the franchise compared to Awakening.