Wow this is a hard choice.
Hm...well here's my thoughts on all the final boss themes:
[spoiler=My Thoughts]13. Fire Emblem 1
+Funky Beat at the start
+Still retains a bit of funk after the epic start
-Repetitive high pitch sound at the start
-Horrible sound font after start (like a bee buzzing)
12. Radiant Dawn
+Sounds somewhat epic (trumpets, choir)
+Sounds mysterious
-A bit too peaceful for a final boss theme, especially against A GOD
11. The Sacred Stones
+Whistle
+Drums
+Some atmosphere
-A bit too all over the place
10. Sword of Seals
+Organ
+Is that a choir I hear?
+Dark atmosphere
9. Genealogy of the Holy War
+Sounds...hopeful...yet overwhelming, it's quite odd and exciting really
-Not quite as tense as the following themes...
8. Blazing Sword
+Harpsicord
+Tense atmosphere
-Starts off a bit dull
7. Thracia 776 (Applying Justice)
+Incredible atmosphere
+Epic drums
+Organ creates tension
6. Gaiden
+Creepy
+Enigmatic, supernatural feel
+Nice instrumentation
+Heavy beat
5. New Mystery of the Emblem
+Nice Choir
+Nice Violin
-Drums felt a bit uneccessary
4. Monshou no Nazo Book 2
+Nice melody
-Doesn't set quite as much atmosphere as Book 1's theme
3. Monshou no Nazo Book 1
+Sets a nice end game atmosphere
+Kick ass theme
-Sound is a bit irritating to the ears at times
2. Shadow Dragon
+Epic intro then you get blown away by...
+HEAVY-ASS-BEAT (SWEET RAVE PARTY)
+Violins
+Bells
+It sounds generally amazing
+/-The demented sounds
1. To Challenge Ashnard
+HOLY-listen to that choir go!
+Minor use of Bell
+Heavy drums
+Generally great orchestration
-Random slow downs
In short:
BEST is FE9 (I'm surprised it got two votes for worst)
WORST is FE1 (Wow that's an irritating sound font)