They are unquestionably separate stories in the sense that each of them is a mutually exclusive “what-if” scenario (hence the Japanese subtitle) following from a single starting point. At least one of them – Birthright – is generally acknowledged to be competently written albeit pretty standard fare for FE, and given my own preferences in narrative for this series I’m willing to cut the other two a little slack even if their plots are hot garbage. I like FE stories that diverge from the typical story of “country of main lord gets invaded by foreign country, lord must travel the continent recruiting allies in order to defeat the main antagonist, something something dragons and/or other supernatural entities.” Conquest makes you the invading foreign country which really deserved to feel more awesome than it does in practice, whereas Revelation throws out the whole binary politics from the start (or at least it claims to) and runs on the power of friendship and tedious map design. FE14 as a whole is the “you tried” game to me, whether I’m talking about story or gameplay or queer representation.
You know, now that I think about it it’s a little odd that I often compare Fates to the Oracle games from The Legend of Zelda, two separate games marketed and sold together that can be played independently or in combination for the full story – and yet while when I was doing my Zelda ranking I had no qualms about ranking the Oracle games separately when I’ve contemplating doing a similar series for FE I just can’t see myself breaking up Fates into its separate campaign. I don’t know what that says about how the fandom has agreed to treat the game or how I prefer to critically approach it, but it’s an interesting consideration.
(Incidentally, neither Awakening nor Fates would be at the bottom of said hypothetical list. Kind of lower middle is a good place for them, I think.)