iirc the Sauron thing applied to War of Elemental, not Fallen Enchantress.
FE is the game War of Magic was supposed to be, so I don't see how the Sauron thing would be less influential now. WoM's problems were legion and iirc, one of them was that champions were underwhelming compared to trained units.
It also doesn't mean Champions won't still be able to take out armies, they just won't be able to do it without specializing in that sort of thing. A warrior would be able to cleave through multiple enemies (similar to now), an Assassin would be able to dodge most attacks until they wore the enemy down, a mage would blast them apart, a defender would laugh at their pitiful strikes in an unstoppable march... but each class would BE UNIQUE in how it managed to go Sauron. Unlike now which is just.. *whack* *everybody dies* for all physical classes. It's friggin boring and has no flair.
Defender, Warrior, Assassin, Mage... but we have those classes and they work the way you're describing. The problem is that the level of your champions is so much greater than the level of your opponents that it doesn't matter what you do because your guys are invulnerable. You've made your champions into demigods; which is pretty much the point of the whole game!
Of course, if you've outclassed your opponents to the point that there's no challenge then that's boring. I fail to see how making it take seven extra turns to finish off a unit will make it more fun.
Perhaps you should play on a harder level of difficulty?
I do think this does highlight an issue with the AI, though: it doesn't really understand how to use spells or use units in combination in the tactical battle. It's battle plans are basic and wrong-headed, (e.g. focus-fire on the weakest and least threatening units) and it completely fails to use its magic effectively to undermine your strategy while enhancing its own. For example, if it slowed and shrunk/withered/cursed your champion, that would give its regular units a chance to apply a beat down.
Making the AI smarter is a huge challenge, granted. But I highly doubt nerfing champions is the solution to making the game more fun.