I've mentioned this issue before, but i feel it needs highlighting again, considering changes to shieldwall and henchmen in the upcoming patch.
I believe the biggest balance issue in FE at the moment, is the ability to infinitely stack "aura" abilities. That is, things that boost your army, such as Shieldwall (+3 defense to whole army)
+3 def on an army is quite reasonable, and it makes a nice ability. But if you put another unit in there with the same ability, your army gets a total of +6. This can stack up to a total +27 defense for a whole army, just from that skill. That much, or slightly less, is enough to protect reasonably from just about anything. Most notably, it gives a large amount of defense to things that ordinarily have little or none, such as beasts and juggernauts, thus mitigating their weaknesses, and homogenising the entire unit roster.
Aside from shieldwall, the other major problematic ones are the Trainer series (increased XP for entire army) and the Guild Grocer HP bonus
With abilities of these sorts, the most common and accepted method of balancing them is to make them unique. ie: non-stackable. Having one shieldwall would give +3 armor, and having two shieldwalls would still only give +3 armor. This provides more reason to diversify your army, and also allows those abilities to be made sufficiently powerful as to be useful individually.
at the moment the stackability is a problem compounded by henchmen, as they have the ability to start off with shieldwall, and an XP boosting ability even at lv0. Because of the way they don't split xp with the soverign, you can make an army entirely of henchmen, and give each one the entire trainer series plus shieldwall, resulting in an army that comes out of the gate with unfairly high defense, and levels about 3x the speed of anyone else.
While it can be funny to make an army of lv30+ heroes with relative ease, it also makes lategame wars a bit of a joke.