I guess my view is: there are many layers to a conflict. (I was going to say there are many layers of strategy, but the layers really extend above and below strategy proper.)
At the lowest level, there’s technique: say you're a skilled man-at-arms. You are, strong, skilled with lance and sword, and agile in the saddle. Your view of warfare is that it's a contest of skill at arms -- the better warrior is the one who can prevail in a duel. Let's say a tactically skilled enemy commander manages to outflank your acies. Now you're facing enemies in front of you and behind. Hey, that's not fair -- it's not a contest of skill at arms anymore. You could have better technique with a lance than either of your foes, yet still get stabbed in the back by whichever one you're not facing at the time. Why don't your enemies learn to fight better -- really learn to wield their lances and ride their horses skillfully, rather than relying on cheap tricks?
Alright, so better tactics seem unfair to someone focused on technique. That tactical commander, though, might quickly find it very unfair if the enemy didn't face him in pitched battle, but kept the main body of his army in on fortified terrain, laid ambushes for his scouts and foragers, and raided his supply convoys, reducing his army to the verge of starvation and desertion without a battle. That's not fair -- the war is no longer about who's a better battle tactician. Why doesn't the enemy learn better tactics and face them in open battle rather than relying on cheap tricks?
The skilled operational commander, meanwhile, might find it quite unfair if his entire country were diplomatically isolated and facing a grand alliance of enemies. If the enemy's superior grand strategy and diplomacy have gotten them into a completely untenable geostrategic position, then perhaps no amount of skill at the operational level can save them. It's not fair -- it's no longer about who's the better operational commander. Why doesn't the enemy learn better operational strategy and learn to defeat their enemies with roughly equivalent logistical bases, rather than having half the world at war with one small kingdom?
Now, not all of this is really in M2TW. For instance, unless your enemy is in a fort of settlement, you can't beat them by starving them. Diplomacy tends to be a bit iffy. Technical skill in battle exists, of course -- a chivalric knight seems to be a more skilled warrior than a mailed knight, for instance, and a mailed knight in turn seems to be more skilled than a mounted sergeant, and units gain experience -- but it's rather abstracted and beyond much the player can do, other than deploy the best units available. (It's not like Mount & Blade or something, where you personally can become awesome with a lance in gameplay.)
The decision to auto-resolve or manually play a battle is a choice you make at a sort of weird place between the two main layers of the game -- the global strategic layer and the tactical battle layer. Just as there are options available to a real Medieval commander that aren't really available to an M2TW player (e.g., as I mentioned, interfering with the food supplies of an army that isn't ensconced in a settlement/fort), auto-resolve is an option that is available to an M2TW player, but not a real Medieval commander. You could choose to always auto-resolve. Or you could choose to always fight battles manually. Or you could have some "role playing"-type rule like "the faction leader's stack fights battles manually, all others auto-resolve". Or you could try to make the optimal choice from the standpoint of strategy, auto-resolving or fighting manual battles depending on circumstances -- this last option being my initial topic.
In my view, excluding a core gameplay option from the purview of strategy because (for that one battle), it isn’t a match of tactical skill is just an extension of the viewpoint of the man-at-arms from the beginning of my post who thinks that battles should be like a series of jousting tournaments or duels, and that the use of tactics to interfere with the pure “fair” contest of technique is cheating.
(For what it’s worth, in my experience a lot of people playing multiplayer Mount & Blade do seem to regard the use of tactics as cheating. They’ll chat stuff like “3 on 1? Pussies.” in chat in a Team Deathmatch.)