I guess what I like about the ZOC is it keeps units from casually strolling past enemies to get into a flanking position. If there is a break in your line big enough for one unit to pass, do you really think the two on either side should let him past to get to your archers? I can agree it doesn't make as much sense to have AoO for moving out of ZOC, but it could be used to exploit in the same way as moving through. I also see it as a retreat-penalty mechanic, presumably you've got to turn your back if you're running away.
Consider though that, ZoC in D&D is about 5 feet around the unit in question, where as a square in WoM tactical combat is enough to hold 12 troops. On top of this, the average moves per turn for a unit is 2. This is not enough to simply move through without still being in attack range at some point for most units. As for the retreat-penalty, this would be something better placed when a unit actually retreats from combat instead of moving out of combat range.
Nice idea, I haven't tried your mod yet as I've been busy putting together an outline for my own and don't want to be influenced. Being objective I have to ask if gaining more powerful attacks with a longer cool down is actually significantly different from a replacement attack, that crops up less often. If the special attack was much more effective in some situations than others, then the player would have to balance whether to waste the special attack and wait a long time for a new one, or perhaps wait for the right opportunity for maximum damage that might not come. I'm thinking about bonus damage vs multiple units / unit configurations / unit types.
I understand the idea of not wanted to be influenced by other mods, but you should take a look at the mod post as it outlines all of the abilities for each weapon. Some weapons do have ultimate attack which are more powerful than their normal attack, but others have knockbacks, chances to lose turn, and stat debuffs. Thus, for instance, A player might choose to use their debuff attack in the openning turns to gain an early advantage, while other might wait to use them to dampen an enemy push.
*Gasp* The Special Abilities Guy was pushing for more special abilities? Now, that's suprising. Seriously, though, while I do agree with most of this, I would imagine that for tactical combat to be deep and fun, this would have to be one change of several. Honestly, I think that you get to a point of diminishing returns and to where they no longer feel "special" pretty quickly.
I have personally made around 60 special abilities, and while after a while there is some sameness, there is more than enough to difference to fill out all of the weapons 2 or 3 fold. In all honesty, this was not the only thing that Derek and I discussed, but was merely the one thing I would change if given the chance to only change one thing. In general, most of us have become a bit spoiled with respect to tactical combat and have forgotten that a simple tactical model can be both fun and engaging. We look at AoW or HoMM and point out how deep those games took their tactical experience. Yet, we forget that games like fire emblem, advanced wars, and shining forces all give incredibly engaging tactical combat with incredibly simple mechanics.