With wandering monsters, I like to have certain "iconic" monsters for each area (such as werewolves in the Blighted Forest and Ankhegs in the Sunken Hills, etc), rather than a mixed bag, as it gives those areas a more distinct flavor.Now it's true that a six-mile hex is pretty big. But in terms of hunting ranges of the sort of carnivores that might be interested in an adventuring party, it really isn't that big. As xkcd reminds us, a 6-mile hex is about 40% of the hunting range of an adult male mountain lion. I think Guns, Germs, and Steel cites 1 person per square mile as a rough support limit for hunter-gatherer societies, so it would take about a full hex to feed an unsettled orc warband (presumably an important difference between an orc village and a warband, besides size, is in livestock and pastoral practices).
With all that in mind, and with simplicity at stake, I think I really don't mind changing most hexes to 1 "real" lair per 6-mile hex. You can backfill with location-restricted undead (wraiths bound to their deathsite, mummies trapped in their tombs, ...) or giant catfish, stirges, giant leeches, and other detritivores and parasites if you're so inclined.
When rolling an encounter in a monolair hex system, roll a d8. On a 1-5, it's an encounter with monsters of the hex's lair's type. On a 6-7, roll another d6, and index that into the adjacent hexes. On an 8, it's a transient from the encounter table for this terrain type. Again, if we're looking at big carnivores, they're going to have hunting ranges and not just stay in their hexes. Climbing Wyvern Peak will probably get you eaten, avoiding it by a wide radius is probably safe, but passing near it is a gamble.
At first look, this change seems likely to make the wilderness game easier for players, because there are fewer lairs per hex to clear. I'm not totally sure, though, because the lairs that were removed (dumb beasts) were mostly not the difficult wilderness fights; they were just grind (and I'm all about cutting out some grind here and there). Further, reducing monster counts also tends to reduce treasure, so it cuts both ways. Monolair hexes do remove the case where you have three orcish villages in the same hex, and they cooperate against you (or you play them against each other), so that might be worth adding back in in some capacity (maybe for beastman hexes, place 1d4-1 min 1 villages). Honestly I wouldn't feel too bad about doubling the numbers on most lairs in monomonstrous hexes; it's still not as rough as a swamp hex with six lairs in it.
While the average difficulty of hexes falls, the variance increases under this system. Some swamp hexes are going to be nothing but 20-foot centipedes with the heads of great white sharks, and some swamp hexes are going to be nothing but nymphs. Sounds like a fine place for a domain seat, no?
This change also produces big gains in wilderness legibility, both for players and DMs. As a DM, I can go "OK so there's a dragon in that hex and there're two villages of orcs adjacent, the orcs are probably subservient to the dragon", and I can show that on my hexographer map with drawn lines in Political mode. With multiple lairs per hex, visually representing that sort of thing is not viable without going down to 1.5 mile hexes. I can also start using a representative hexographer monster icon per hex, and removing it when the lair is cleared. I was already doing that on 1.5 mile scales, but making that work on 6-mile scales would be nice.
With a lower lair density, it becomes relatively easy to have treasure maps point primarily to sealed undead sites - there's plenty of space in those hexes, and the area around the barrows or whatever is haunted so the main lair leaves it alone.
It might also be worth considering generating two or three "lair features" per hex - ruined fortress, abandoned mineshaft, cave, grotto, Weathertop, and so forth (ACKS page 289, or some results from Wilderlands of High Fantasy pages 3-8), which persist across lair clearings and are repeatedly reinhabited when the region restocks. This makes for good reuse / recurrence of places, and also allows for some combinations that you might not see otherwise - a fortress full of ankhegs, a mineshaft of nymphs (quest time - liberate their grotto from whatever drove them out), a giant anthill now inhabited by goblins (who wear carapace armor and bug-face helmets), and so forth. If the shelter's good, something will live in it. This also limits the number of places the players need to check, making reclearing hexes quicker because you don't have to search the whole area (probably), just a scant handful of notable sites.