I posted this in response to Sean's thread here, but I think it deserves its own post.
I've been thinking about the way that the three trees interact with each other for a while now, and it seems to me that the best way to implement them (going by how they're currently designed) is to more or less make Civics the city and troop size tree, Warfare the arms and armor tree, and Magic the champion and spell tree. Civics, I think, is in a pretty solid spot at the moment. Magic, in my opinion, is the jack-of-all-trades tree; if I invest fully into magic, I can enchant my cities, champions, and ordinary troops into unstoppable powerhouses, learn to train ordinary soldiers with magical arms and armor (which is almost always simply better than the weapons I could use from the warfare tree), AND be able to hire better heroes and go on more dangerous quests. Warfare... gives me leather armor. And currently, that's all I need it for. Bear in mind I've mostly been playing on Easy (though that will change in my next game now that I actually have a fighting chance against monsters), so I can't say for sure whether my admittedly one-sided games bear much in common with what most players are seeing. That said, however, I think the Magic tree should be changed to offer benefits that are more geared towards champions and your sovereign than ordinary armies.
With that in mind, here's what I would change: I would put every weapon unlocked by Enchantment in a new branch of research, Enchanted Arms, requiring Shard Harvesting and Archery, located in the fourth tier of Warfare, moving the Guardian Shrine into Rituals to make room for a new technology, Heroic Arms. This would unlock items like the Toxic Dagger and Guiding Spear, only available to champions and requiring Gildar to purchase from your shops. I would then take all the weapons from Magical Forging, put them into Arcane Weapons, and put that tech in the warfare tree with the prerequisites of Advanced Archery, Weapons of War, and Arcane Mastery in the Magic tree. I think this is fine, considering that all the weapons in both techs either start with better numbers than their mundane equivalents, or scale with unit level. We're gonna just ignore the terrible, terrible Hunter's Short Sword too. Replace the weapons in Magical Forging with tier/level-appropriate champion gear, and put a new tech where Arcane Weapons used to be that does the same thing. Rings, belts, cloaks, etc., and the Monk's Staff are fine where they are, given the usefulness of such items to both trained units and champions (erm, ohai Monk's Staff!)
Considering the current price of the champion items that would have to be used to fill out the holes I just made in the Magic tree, the pricing system of items would have to be re-evaluated as well (nerf base prices and bring back selling them for 50%!) to make investing in this tree worthwhile to players. IMO, this would also give a more clearly defined role to each tech tree (want awesome cities? Go Civics. Need weapons of doom? Invest in the Warfare tree) and give a few more things to spend gold on besides rushing city production (sure, getting the Ironworks this turn would be awesome, but my sovereign would love an Ignys Battle Axe...).
In addition, I think that the Archery technology needs some work. Currently, I get more bang for my buck from magic staves, since they completely ignore armor. I've yet to actually field archers in FE, so inferior are they IMO compared to magic staves. If I knew how to mod the game, I would introduce two bow types per research: longbows, and shortbows. Shortbows would be slightly less damaging than current bows, but have a much lower initiative penalty, a mere -5. Longbows would keep the current initiative penalty, but deal a bit more damage to compensate for their slow reload times. So, when you research Archery, you would get two bows; the Crude Shortbow, and Crude Longbow. The Crude Shortbow would only deal 5-6 damage, but get off more shots per combat. The Crude Longbow, by comparison, would still have the full -8 penalty, but you'd get 8-9 damage per shot from it, making it much more useful against armored foes than bows currently are (assuming you're not Tarth, that is. Who, by the way, would get a further bonus to the favored stat of each bow type). Longbows would be replaced with Improved Archery, which would see the damage of each bow type improve by 2-3 points. Advanced archery would get an additional 2-3 points of damage for the shortbow, and an additional +1 initiative (for a total -4 initiative penalty). The longbow would still be as slow as molasses, but would get a much greater damage bonus to compensate. I'm on the fence about longbows having a small (10-20% scaling) armor penetration bonus.
Let me know what you think.