I don't think a unit cap would be a good idea. It would severely hamper the whole 'chaos' aspect of the game if there was some max limit to the amount of chaos that could exist.
Here are my thoughts on the whole situation:
I'm generally happier if games evolve (it's why I like Arcen games so much), so I'm not upset that things get changed after release.
That being said, I think sometimes a softer touch is better (move numbers around, change mechanics less), and I think the bandit keep immunity to myth is swinging a bit too hard at the problem. A softer solution may be to have bandit keeps be a new 'type' of building, which myth units get a fractional damage "bonus" to (say, 1/2).
I like the keep health reduction because I think these things are too hard to take down, but I also think it's more of a mechanical thing, not a number thing. They are hard to take down because the red and blue dudes like to bypass them too much.
The 'exploit' that was originally targeted is also showing a broader issue I think (and it's something I've been feeling more and more as I play). It's not really just about bandit keeps, it's that myth units are just so much BETTER than the human units. Now, I know you might think "Well aren't they supposed to be?!", and that would be right. However, I've found that when I play my general progression seems to be:
1) build up standard military economy
2) build up economy to support myth units
3) pretty much only use myth units the remainder of the game and don't care if all human units are dead
I'm pretty sure after a few more games my strategy would have evolved pretty much to "go to step 3 immediately" as well.
I kinda hate the human units. They do dumb things, it seems like a miracle if they kill a bandit, most of the time they FEED the bandits (if you are playing with veteran mode on, hard and above), and they block each other pretty much all the time.
I try to play the game I feel I want to play it (and should be rewarded for playing it), which is to build a ton of military units, and then I feel punished because it's such a terrible strategy. Schools help a little, but you are held back by age, and by the time universities open up, I have the resources to throw myth tokens and use god abilities anyway.
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The mountain thing.
I know I may be the minority here, but I like that mountains are gone, but that's more because I dislike game mechanics changing too much between difficulties. I'd rather have mountains available at all levels and be balanced around it, or none at all.
I think a 3 AP mountain/lake cost at all difficulties would be a good compromise. After all, there is precedent for it because ruins cost the same as well.
Blocking things with mountains is not really any more overpowered than using a Cerberus or placing a god token in the way. Bandits cross them anyway in hard, so blocking off your town with mountains in the higher difficulties pretty much makes no sense anyway.