If you don't care about either IP, which is a better musou game? FE or Zelda?
I look at these games as being part of the same series, since the way they play is fundamentally similar, I.E. controlling controlling more than one character during game play. So to me, it goes Samurai Warriors Chronicles -> Samurai Warriors Chronicles 2 -> Samurai Warriors Chronicles 3 -> Hyrule Warriors (DX) -> Fire Emblem Warriors -> Hyrule Warriors AoC. (Samurai Warriors 4 has this too, but that's only two characters whereas these games can go up to four and feel more strategic in that sense.)
Fire Emblem feels more like a traditional musou game with a set story mode. There's more than just story, but that's a separate mode (where it's kind of like FE in that you have a small map with units you move around, but the fights are musou stages).
AoC, like Hyrule Warriors before it, retains elements from the Zelda series and like BoTW, you're on one giant map that you can "fill in" with new quests as you go. These quests are either smaller battles or just providing items/ingredients to clear the quest and get more items, power-ups, or character upgrades (health or combo extenders). It's more grindy than other musou games because of this, since you might need to replay levels or quests to get items or currency. That's not to say that there isn't a grind in some other musou games, but it's more like post-game or other modes for those titles and in this one, you'll want to grind to ensure that you're powerful enough to tackle the main story.
Another thing is performance- Fire Emblem runs better than AoC does, especially with its 60 FPS performance mode. AoC looks very much like BoTW and takes a perfomance hit because of it. It's not bad at all, but noticeably worse than the first Hyrule Warriors and Fire Emblem because of it. Really, those two games are standouts for running so smoothly since most musou games tend to have lower frame rates or framerate issues.
If you want something more akin to traditional musou, go with Fire Emblem. Hyrule Warriors (both games) is a bit different, but in a good way.