Personally I find it odd that the game has so much counter-attacking in the first place. The amount of times you can swing your sword in a minute doesn't depend on how many people swing their swords at you. I get it that they can't have a system where enemy units all attack you in one turn at the same time before you strike back but at the moment it seems almost the other way around: positioning and numbers are irrelevant and it makes little difference whether you take everyone on at once or individually.
Once we get the initiative system though, and split the turn order up into my archers, your dragon, my infantry, my hero, your knights (or whatever), then the potential problem of all of one players units attacking one enemy (effectively) at the same time will be removed, so the counter-attack system will be a lot less necesarry.
Once that happens then we can implement better ways or working out who strikes first, who gets a counter-attack and who doesn't. Personally I think it would be better based on weapon types. If weapons had a Reach stat, this could be used to determine who struck first (say, both sides roll 1-10 + reach + 5 charge bonus and the winner strikes first), and if you beat them by a high enough margin, they wouldn't be able to counter-attack at all. Balance this with a mobility stat that determines how many sides you can defend yourelf from (ie, a spear has a long reach but a mobility of only three, so can only counter-attack enemies in front and on the two squares either side, while a sword has 5 and can defend itself from flanking attacks (and possibly higher basic damage).
Just want to second that I think these ideas sound awesome. Let hope we get something at least this interesting with FE.
Hopefully the weapons types will also be figuring into the initiative system in some way. Spear are long, can successfully counter attack lots of strikes to their front, but they're also slow and hard to move around the battlefield. This type of stuff would bring up all sort of interesting dynamics where formations and maneuvering would actually be meaningful. You really want to be able to flank those spearmen with your swordsmen and if they also get a higher movement order that also makes it possible for them to pull off this tactic.
Another interesting, and pretty obvious, addition, that's missing from WoM right now would be an actual facing system tied in to all this. Are your spearmen facing forward/left/right/back. Changing facing uses up something like half a movement (i.e. you drop halfway down the movement queue instead of all the way down). Thus is the enemies trying to flank you you have the option of trying to counter by rotating some of your own units to catch them.
And all of this brings us to what is probably essential to making all of this really fun: some way to set up your battle formations prior to a fight. Please, please no more random piles of units facing each other. We really need a system where we can place our archers to the rear, cavalry on the flanks and infantry in the middle. Or change it up and drive straight through the center with your cav to split their army in two. Etc.