To say that New Vegas is setup differently than Fallout 3 in this regard is complete and utter nonsense. They both make use of the leveled spawns and encounter zone systems. The DLC's are setup in almost the exact same way in both games. New Vegas makes less use of the encounter zones in the wasteland (which are setup by region) but it still makes use of them in many areas.
Leveled spawns make sense in most cases, but the consistency of an environment shouldn't be sacrificed for it.
Leveling a Death-Claw, Giant Radscorpion or Yai-Gui to Level 50 makes sense, because these creatures are general strong enemies and should be so at all levels.
It also makes sense to level NPCs, Ghouls or Super-Mutants, as having them as strong foes doesn't influence the consistency at all.
However, you shouldn't replace a gecko with a Radscorpion at L20. A Gecko should level until maybe Level 15 and be capped there, but if you replace him with another critter type, you change the entire environment of the region.
For example Geckos are resources. People hunt them for hide and meat. Nobody would hunt a Radscorpion. If now at L20 all Geckos suddenly become Radscorpions, the nearby towns can't survive anymore. Also, if every prey gets replaced by dangerous predators at some point, then the whole ecosystem would collapse.
There are many Open World Games such as Far Cry or all these MMORPGs, that just place predators on every corner to have proper loot and challenge, without questioning if this would hurt the authenticity of the world. I find it very hard to take such games serious.
I'm just suggesting not to throw all world consistency to the dump for the sake of balancing, if you plan to rework the entire level system of all TTW.