I agree that would be nice, but the dev´s have confirmed on several occasions it is never going to happen for FE. The engine is not capable of handling it, or the AI couldn't handle it, or both, I'm not sure. It might be looked at for an expansion, or more likely a sequel if it is ever made.
I disagree it would be cumbersome. It gives the AI an opportunity to put up a real fight. Taking a town would take more than just walking an army up to it and press auto-resolve. You'll either have to bring a second army to intercept potential reinforcements, break off part of the army for that duty and have them back before the battle, or risk facing stronger opposition. This decision alone would make the process more interesting and engaging.
And yes, you'll be vulnerable to nasty spells, as you should be. The solution lies in balancing the spells, either through mana costs, adjusting the effectiveness, or protection and counterspell abilities.
Just imagine; after a long and bloody war, you have finally gained the upper hand. Enemy forces have been removed from your country, and you've gathered an army to end this war once and for all. You send it off to take the enemy capital where your rival, a fire archmage, is holed up with a large part of his army. While you have a few skilled wizards serving you, the only one who can truly protect your army from the enemies firestorms is you, the sovereign. During the siege you are focused on maintaining the shield protecting your army. Your second in command is preparing your troops for the coming battle by casting blessings to protect them from fire. Two other heroes are send off with a small force, to keep enemy reinforcements from his other cities away.
That's just way more epic than sending in a few stacks, maybe have one of them hit with a fire strom, auto-resolve the first few battles, sacrificing a few stacks to grind down the enemy, and then finally send in your killer stack.