First of all, I would like to say that War of Magic's main problem in my mind wasn't a gameplay concern, it was blandness. And that's fixed. Derek and Dan Stern have gotten that taken care of just fine.
But the main gameplay issues that Fallen Enchantress were supposed to fix remain.
The best unit is still the one that you pile all your best stuff on. Once your best stuff starts taking up too much encumbrance, stick a horse under them. This makes your units expensive, but a stack of them is the toughest thing around, no matter what.
Second issue is that champions are still not very important. Champions simply can't match the damage output of a group, and even as capitar, the gold costs are such that hiring a group of soldiers is easier than outfitting a champion. Now, Champions do last longer since they don't usually die, and thus will be better able to get to a higher level quickly. And early on, a dedicated melee champion can be pretty tough. But if a well equipped group gets through the first few levels, it won't die either and will be more effective in combat.
This means optimal strategy is the same as it was in WoM: Make a big stack of identical units with all your upgrades slapped on. Put a champion with them in a support role, with enhancing magic and abilities. But don't bother using tactical magic in most cases, it will turn the tide of a close battle but it isn't enough if you're totally outgunned and it's a pointless waste of mana if you'd win with no losses.
Monsters are very strong early on. I happened to spawn on a spit of land blocked off by trolls on each end and they were able to hem me in. The monsters from quests were also too much for just a couple champions. Later in the game, once some uberunits have been made, everything becomes easy again. A killer stack can wipe out just about anything. Although this could have been an issue with my random start, and not finding more powerful monsters later.
Now, the biggest problem: Tactical battle is not fun. I find myself auto-resolving battles even when they should be exciting. It still amounts to directing your units to go kill the enemy. There's a few little details where you make decisions, like who to kill first and how much mana it's worth expending in this battle (most of the time the answer is zero) but overall there's not much gameplay.
The worst part is, there's lots of things that can be done to fix this which have been suggested on the forums. Mostly they amount to making good tactical maps. Add elevation. Add impassable terrain, and terrain which blocks sight/targetting. Maybe add army facing, to allow for better maneuvering, but only if you can make a good interface and turning system.
Until features like this go in, tactical battles will continue to not be fun, and will only be used in situations where the auto resolve button would cheat the player out of something.