So take this with a grain of salt, but these are some changes that have worked extremely well for my group of friends, hopefully there are others that might find this interesting.
In general i play with two other players and for the most part we have loved the concepts but found a few things off in the three player experience. Very hard to scale to a difficulty that feels right, not very interesting choices when playing, locations not very interesting, too random, and most of our loses when drawing extra cards would just be due to threat losses (which felt like a boring way to die).
So we made a few cahnges, one was simple :
Start with two heroes (these days we deal out 3 heroes and pick 2)
Start with a threat 1.5 * sum of heroes threat
(Made the resource spending more interesting, having less heroes forced more interesting moves in the beginning, and in general we just found the two player game was balanced better)
The other changes are a bit more drastic :
Allow 2-3 active locations
You can travel to one location for every open spot at the
beginning of the travel phase
(Made locations more interesting as locations are not just getting clearedin the staging area. Travel and active lcoation texts actual matter. Also allows you to flip more cards without locations burying you without a northern tracker.)
Seperate the quest resolution from the quest phase, and resolve the quest after engaging and travelling.
( Allows us to react slightly to what cards get drawn, less random, generally do not lose to threat >50. )
Draw 3-5 encounter cards per round.
(Depending on how difficult we want the quest to be.)
Now this isn't perfect, but considering what we are changing it doesn't break the game as much as you might think(besides Dul Guldor). That being said beware, the games will tend to last longer and treachery cards become probably too powerful. But we have loved it so i thought i would share. These of course can be fitted to 2 or 4 player quite easily.