Well said.
I agree. Regions should have varying difficulty and creatures should be "spawned" in a more logical way.
This could quickly get out of hand. In Oblivion it's possible to make many creatures appear out of "one" Leveled Creature List, but only if the level designer wants to make it so. It should stay that way.
In general, I like the concept of "Leveled Lists", because they can be used both as a way of balancing encounters AND/OR randomising them. Morrowind had level scaling and few people complained about it, because it was much less drastic than Oblivion's one.
It should be level designer's decision where to put leveled lists (and which ones) and where to put hand-placed creatures (and which ones). In some places the level-designer may want to put only dremoras instead of all kinds of Daedra or he/she may decide that in a given room atronachs would be much more interesting type of enemies than clannfears or scamps. There are moments when unique, unscaled enemy is the best option, accompanied by two leveled opponents (with level caps) for balance. It all should serve some purpose. The more variety there is, the better. The more balanced things are, the better. The more "seamless" the experience is, the better - that's why scamps shouldn't disappear from the game's world after a given level etc.
Each cave/fort/landscape type/whatever should have a little "something" (sometimes it may be hidden) to make it more fun to explore. An unique rock formation, interesting lighting or unique sounds for the atmosphere purposes, funny "packs" of trees, mystic ruins surrounded by thick forests etc. Even if things are randomly generated at first, it will feel good if the level designer steps in and make one in three cells unique in some way. Possibilities are numerous.