I wasn't entirely sure if the question here was "which plot is the best" or "which plot was told the best" so I voted for FE5, as the one I feel was told the best. I think that FE4 has the more interesting story to tell, and based on that alone I might say FE4 is the best. However, I feel that FE5 conveys its story so much better in almost every way, so it gets my vote.
While its not another "saving the world" plot that you can find a variation of in literally every other Fire Emblem game ever made, I think the smaller scale does FE5 a lot of favors in terms of characterization. It knows what it's supposed to be from the beginning: an underdog story. The game pounds it into your head time and time again that you are vastly outnumbered and in way over your head. You spend a large part of the game on the run, which realistically more FE Lords should be doing instead of charging in headfirst.
Because you're playing the underdog, each victory feels like you really earned it, and I'm not talking from a game play standpoint either. Even when you go on the offensive in the story, its almost always credited to superior tactics, rather than brute force, and the game makes it known in-universe. Without your tactician, you're boned, and the game sticks to that until the end.
FE4 was pretty good about its worldbuilding, at least in Gen 1, but I feel like FE5 does just as well if not better for its own story. In FE5 we get to see the Loptyr Empire being assholes instead of just hearing about it. We get more information on the Thracian people, and really get to see firsthand that even though the country is technically unified, there's a LOT of problems going on behind the scenes. We get to see a lot more people who are good men/women manipulated into working for this corrupt system, whereas FE4 had Hannibal. And this isn't me trying to shit on FE4's plot, quite the opposite actually. FE4 had a pretty good plot and it's not entirely fair to say FE5 did it better when it wouldn't exist without FE4. Regardless, the fact that FE5 takes this established world and brings it up close as if under a magnifying glass really does a lot to create a more cohesive narrative. I don't feel like the story glosses over things because there just isn't enough time to explain all the relevant information without a 30 minute text dump at the end of each chapter. And really, that is Thracia 776's greatest strength when it comes to the story. Because the story itself isn't as grand, there's enough time to explore the details.
On a side note, while I'm not trying to take away from the other games, I really wish more FE titles wouldn't be afraid to stray from "Lord beats empire, fist fights God, bangs (sometimes a dragon) girl, The End" type stories. I'm not knocking it because it's a cliche, but because the more I think about it I genuinely don't think that Fire Emblem is a good platform for telling these kinds of stories. Generally, the only way to learn about the world in FE is to read about it. It might be Pre-Chapter Dialogue, visiting a house, support conversations, or whatever. The bottom line is, that's all you can really do with it. There's really no exploring the world yourself, unraveling of mysteries, or any of that stuff to flesh out a world/universe besides reading text boxes. Writing a more personal story doesn't necessarily fix any of that, but at least then the narrative tends to be more focused on the characters themselves, rather than a bigger picture that is often hard to grasp the way its explained in game. On the flipside, for a series with so many recruitable characters in each game, a large number are surprisingly well thought out, and tend to be at the very least 2-dimensional. Maybe IS should try another game where the characters drive the story (like FE5), rather than having the story drive the characters?