Thracia was robbed! ROBBED! But it's not surprising, it didn't sell well. If all sales were equal, it might have been up there. A Tellius game would have been up there too if those games had sold well, though I don't actually care for Tellius as much as most people. I'm happy to see FE3 on the list, but that probably has something to do with it having sold well.
Not that it matter, but I do love ranking things, so here are my rankings. Don't look at the letters of the tier list and think of those as a grade for the games. Sacred Stones is in my C tier, but I wouldn't give it a C. The tiers are just meant to represent that games in a tier are close in how much I like them, but there's a gap (sometimes big and sometimes small) between tiers.
S tier:
1. Genealogy of the Holy War
2. Thracia 776
Both of these games are masterpieces. I absolutely adore them. Play them blind if you can, it's okay to miss things, you're going to be fine.
A tier:
3. Shadow Dragon (Fight me irl, except not really.)
4. The Blazing Blade
5. The Binding Blade
B tier:
6. Mystery of the Emblem
7. Radiant Dawn
C tier:
8. Sacred Stones
9. Path of Radiance
10. Awakening
D tier:
11. Shadow Dragon and the Blade of Light (This is 90% because the music is amazing.)
E tier:
12. Conquest (People say the gameplay is great, but it still has pair ups and I don't like that mechanic. There are some good maps, but they get much worse in the last third of the game. Of course the story is horrible.)
13. Gaiden
14. Shadows of Valentia (This should probably be above Gaiden. I'm not a big fan of either game, but Gaiden has a charm to it that Shadows of Valentia lacks. But also I prefer Mother 1 to Mother 2, so why are you even reading this? Don't listen to me.)
15. Birthright (To be fair, this game probably should go higher, or maybe it should go lower. The thing is, I don't remember anything about it. It's the only Fire Emblem game I can say that about.)
F tier:
16. New Mystery of the Emblem
17. Three Houses (I'm not trying to be a contrarian here. I didn't like it and I had to play it four times because I won't let Fire Emblem stone will go unturned.)
18. Revelation (Fun fact, there's no s at the end of Revelation. I'm not trying to make a joke or sound pretentious, I legitimately think that of the five people that read this, three of them might go Google the name of the game and be like, "Oh you're right. Neat."