Most of the problems here will be resolved according to the journals of what will happen in the 1.1 patch.
For example, the bear does come late in the game compared to it's strength, but after global essence and maintenance cost will enter, the bear might be a good creature because of his low cost.
Same thing with every comparison between summons. If one will be harder to maintain, the player will have two good options to choose from, one cheaper the other stronger.
I'm guessing the option for monsters when the city levels was placed there mostly to supply an alternative to cities that have no gold, tech or arcane building next to them.
There are many good suggestions for this in the forums, hopefully one of them will be chosen.
As for the monster lairs, maybe it's just me, but I prefer the game to be between champions and regular units with monsters as a bonus, and not the other way around.
Your idea can and should be implemented, but I think that it should enter as a mod, and not as a general game concept.