Control is another reason. In a dungeon, there are boundaries.
Exactly...the wilderness lacks walls.
Walls let the DM channel the PCs to discrete encounters. As suggested earlier, PCs can completely bypass a wilderness area because they passed two miles to the east of it, and never saw the ankheg lair.
The wilderness also lacks the "dungeon level" concept, whereby dungeon "levels" can be discretely designated to challenge a given level of PC. We could designate the Bone Hills as fit to challenge PCs of levels 5-7, but that doesn't stop them wandering off from the Bone Hills into Dagger Canyon and meeting those CR 21 encounters that were supposed to be saved until much later in the campaign. <- that's an extreme example, but illustrates the point.
Without a hex map, the wilderness also lacks discrete areas which a DM can assign an encounter area number to. And it's also generally far too big to populate entirely, because worldbuilders love to pack on the hundreds or thousands of miles.
Add all this together and you can see why wildernesses are traditionally very much secondary to the dungeon environment. The shortcomings of the wilderness also throw into sharp relief what could be considered one of the secret weapons of D&D that has kept it out in front for all these years; the dungeon provides a very good "game board" for an RPG, because it guarantees a certain amount of transparent railroading that seems justified rather than forced: "You can't go there; there's a wall in the way." Even GMs of games like Shadowrun and Vampire: The Masquerade borrow this dungeon model of play occasionally because it's so useful in controlling the game.
To date, I don't think "the collective D&D conciousness" has come up with solutions to these problems...it even struggles with the existence of high level good NPCs overshadowing the PCs, and basically glosses over the notion of PCs running into a status quo encounter which the PCs have found which is far beyond their ability to deal with. (MMORPGs only seem to handle it by some sort of indicator of how tough the creature is relative to the PC.)
Eberron's "mostly no high level NPCs" policy indicates that designers have paid at least a little thought to such things, but there appears to be a lot further to go. I don't know solutions to them apart from: use a hex map, keep the wilderness small with boundaries around the edges (e.g. put it on an island, in a rift canyon etc.) and arrange the wilderness areas such that higher CR challenge areas are progressively further away.