The group finally gets Nyna after she has spent an entire game (plus this one) as a non-combatant. Sure enough her bases and growths are shit, and she (like the other clerics) should be instantly moved away from combat. Actually, this makes sense — Nyna wasn't raised to fight, she was raised to rule.
The other three (Maria, Lena, Elice) as well are also pretty weak in this game despite having all sorts of badass potential in the first game. They spent the entire events of this game Brainwashed and Crazy — so naturally they won't be ready to fight, they're out of shape.
This actually can be applied to Matthis as well. He's ultimately just a random civilian who is forced to fight — why should anyone expect him to be good at it?
Why Frey couldn't be revived in Shadow Dragon despite being the canon sacrifice. (And thus Marth's motivation for acquiring the Aum staff) This game confirms that yes, he was the sacrifice, but as for why he's alive, it turns out, he was left for dead but rescued by some nearby civilians. Thus, Marth could not resurrect Frey with the aum staff... because Frey wasn't actually dead! That's actually some very brilliant Foreshadowing.
Palla and Catria are quality units in this game, being much better than they are in the Shadow Dragon. This could be explained because they were polishing their fighting skills during the war in Valentia beforehand. Est suffers from Bag of Spilling due to not having as much practice caused by her retirement from military service.
As mentioned in some other Fire Emblem pages' Fridge Brilliance, Jagen's status as a Crutch Character is explained by the fact that he's past his prime, while the others are in their prime. So why does Arran fit under this? Well, he mentions it as the fact that he's sick and dies of his illness not long after the war ends. Of course he won't be at his prime; it's actually a neat form of Gameplay and Story Integration.
Some of the Starshards makes sense with who held them:
Toras and Gemini: He is accompanied with another Ballistician, making it close to the "twins" theme of the constellation.
Lang and Cancer: Lang's tactics in his boss fight involves flanking the Altean army in a pincer attack. As a General, he is armored from head to toe like an exoskeleton of a crab. Alternatively, he is the blight that tarnished the name of Archanea with his heinous acts, fitting another common usage of the word.
Jeorge and Sagittarius: He is a renowned archer.
Hardin's lack of screentime in Shadow Dragon despite being a prominent figure in the Archanean League makes more sense with his Motive Rant towards Marth in Chapter 20 of Book 2; Nyna handing over the Fire Emblem to a young newcomer to the league and spending more time with said person while Hardin himself was ignored has likely fueled envy within him.
The original version of FE3 has some hints that the Wyvern mounts are descended from insane Manaketes! Brr!
FE12explicitly states it.
The Avatar from Awakening, which takes place ages after New Mystery, is revealed to look very similar to New Mystery's avatar in a DLC encounter with Marth. Said "new" avatar is destined to serve as Grima's host. What on earth happened to the first avatar to get that kind of a fate pegged on to his/her possible descendant/reincarnation?
Echoes also confirms that the Avatar is likely a Generation Xerox.
