Why is Dark magic usually confined to a handful of characters? It's actually hard to use, and it apparently is easy to become corrupted by the lust of pure power. In addition to the social stigma (Canas and Knoll insist it's ancient magic, not evil magic), there's very few people who teach it, and most find it easier to learn Anima and Light magic instead. (Also, there are no real risks to Anima and Light magic, while Dark magic is very dangerous to wield as proof, Canas mentions his brothers becoming soulless husks.) So, the combination of stigma, few people who can teach it, how tough it can be to master yourself, as well as the fact that learning said magic is quite literally do or die, and that's why there's very few dark magic users around.
Almost every main character is nobility or royalty, and they find this out early on. This is probably to give troops a reason to defer to them, and why the main character can command troops to begin with. People command armies either through experience and skill or inheriting the post. It's why the unexperienced character can command troops in the first chapters. In Shadow Dragon and Mystery of the Emblem, Marth is a prince, so he can command (in Mystery of the Emblem, he's also an experienced leader). In Gaiden, Alm is the lost prince of Rigel, but doesn't discover it until the end. However, before that, he is thought to be the grandson of the Golden Knight Mycen. Celica, in the meantime, begins as a warrior priestess, and is then revealed to be the lost princess of Zofia. In Genealogy of the Holy War, most of the playable characters were nobles, but they followed Sigurd for various reasons (Azelle wanted to rescue Edain, Lex was along for the ride, Quan vowed to help him, and Ethlyn was his sister), and they followed him for his cause later. The second half was because the characters wanted Seliph to ascend the throne. Most of the Army of Thieves and Whores in Thracia 776 followed Leif for a lot of different reasons (from ideals to payment to not being executed), but Finn trusts his prince's judgement and Evyel trusts Finn. In The Binding Blade, Roy is the son of Lord Eliwood, thus making him a commander of the Lycian League, plus he's explicitly filling in for Eliwood, who is unable to fight or command due to illness. He also gains a lot of authority when he becomes the protector of Princess Guinevere of Bern. In The Blazing Blade, Kent and Sain started out protecting Lyn, and followed her to help her save her grandfather. In The Sacred Stones, Eirika pretends to be a mercenary named Erina at first, while Ephraim leads a guerrilla force of Renian knights. By the time they reunite, both are backed by Frelia's forces. Ike's not a noble, but the Greil Mercenaries follow him since he's Greil's son, so this counts (Shinon and Gartie are noted exceptions). In Awakening, Chrom is fairly seasoned; the Shepherds follow him because he's the captain, not because he's the prince.
If you think about it from a realistic perspective, the weapon triangle makes complete sense. Swords beat Axes because Swords are more graceful and less clumsy than an Axe. Axes are effective against Lances, simply because an Axe has the power to snap a Lance in half. Lances beat Swords because of their longer reach and ability to hit more vital parts.
The Artificial Stupidity can be largely explained by the fact that a lot of the enemy platoons you fight are headed up by General Ripper types who will eagerly execute their men for even the slightest hint of insubordination. Sure, blindly charging at you will most likely get them slaughtered, but not blindly charging at you will certainlyget them slaughtered. (This doesn't help explain it when the enemy commander is not the sort of guy who'd do that (Camus, Mustafa, et al), but those tend to be the exception rather than the norm, and they more often than not have superiors who do fit the follow my every command to the letter or die horribly mold.)
How thrown in Marcia and Tanith's A support seemed. Tanith thought Marcia had so much potential to be commander of the Holy Guard that she swallowed her pride and admitted it? Really? Marcia? She never really struck me as uh, a leader type. But then sometime later I was looking at her behaviour around Makalov and realised how much she was acting like Tanith (just with Unusual Euphemisms). That's the potential Tanith sees in Marcia! The perfect successor!
Ena is almost killed by the Black Knight after her failure to stop Ike. The Black Knight confesses that he did not deliver a clean blow despite stating that he would execute her. If Ike does not defeat the Black Knight in Chapter 27, Ena is recruited instead of her grandfather, Nasir. Ena comes automatically equipped with the skill 'Miracle', which nullifies lethal blows.
Ranulf is a very slow and very defensive unit, completely at odds with the archetype of cat laguz. However, after seeing the character archetypes that the beast laguz actually exhibit (cats being aggressive and combative and tigers being laid-back and (relatively) pacifistic), Ranulf certainly fits more into the latter, and shows no traits of the former. If he's not going to act like a cat off the battlefield, why should he on it?
Ashera is the goddess of order, which is, of course, why her biorhythm does not fluctuate at all.
Why, when the Valkyrie's Magic stat cap is so much higher than its Strength stat cap, is Mist only able to reach SS-rank in swords? Well, because she's Greil's daughter.
Part 4 involves The End of the World as We Know It caued by a mad goddess and efforts to reverse it. Why, then, would the survivors split into three groups? In Fire Emblem, you have the best Quality of troops versus the best Quantity of troops the enemy brings against you, therefore grouping all your troops in one location is just begging for all the enemies to gang up on the weak link, or any link at all, and wear them down until they die. Therefore, splitting up in teams is the best way for the player army to fight the much larger enemy army by forcing them to split down and lose the advantage of numbers without you losing your advantage of quality. Splitting into three armies is just a larger-scale version of that.
It may be a bit weird to see an enemy having mastery of Strike weapons, as the enemy in question is basically a mage. But that enemy is Ashera, one half of the creator Goddess of the world. This is a play on that fate-tempting line:
Some people were disappointed that Ike didn't marry Elincia as per convention for every Fire Emblem series of the main character getting hitched with the princess. The reason was pretty simple. Ike's father was a Daein Knight and people would know that Ike is by blood a Daein. If Ike asked for Elincia's hand in marriage, he would have caused a political incident that could spark another war. So both backed off from any idea of a marriage, let alone an affair.
Additionally, Ike hated being a noble for the brief time he was one in Path of Radiance, and renounced his title and went back to being a common mercenary as soon as he could. Elincia, meanwhile, is the best Queen Crimea could ever ask for, and an entire part of Radiant Dawn is spent showing how fitting she is for the role. For them to be together, either Elincia would have to give up the throne, which would be very bad for Crimea, or Ike would have to become a noble and live at the palace, which he'd hate. Circumstances mean a relationship between them couldn't work.
Plus, Elincia can get her own Knight! And it's Geoffrey, who's had a Bodyguard Crush on her for a long time and is far more used to noble life than Ike will ever be.
Also, Elincia fills the same role as Nyna and Guinevere, as the princess in exile who the heroes helped to restore their respective kindgoms and never end up as the main character's love interests for reasons such as political issues or the princess already has someone in mind.
In the Tellius duology, Ena's overall stats are weaker than you'd expect from a Dragon Laguz, but the epilogue of Radiant Dawn reveals that she's been pregnant with Rajaion's child the whole time. Her stats are what they are because she's holding back on purpose so as not to endanger the baby. Especially since Rajaion dies and that baby is all she has left of him.
Ike and Soren's (and to a lesser extent, Soren and Stefan's) supports reveal that Soren is a Branded and the Laguz effectively ignored his existence as a child. Why then, did Lethe and Mordecai acknowledge him when they met? Soren was with Beorc. Those Beorc were willingly traveling with Soren, so to the Laguz that clearly meant they could not have known what he is. They had to acknowledge him, because otherwise they'd be forced to admit to one of the greatest secrets of the Laguz.
Fridge Brilliance in that it explains why Lethe is especially hostile with Soren, even after she warms up to Beorc slightly.
Fridge Horror that has permeated the fanbase in the Tellius series: Soren is Branded. Branded age slower than beorc. Soren has a beorc around his age as a Living Emotional Crutch and Only Friend (at least). That's unlikely to end well.