How about a rule to scale the game better for more than 2 players?

Setup Hand modification:

for 3 players, each player's setup hand is 5 cards (instead of 6).
for 4 players, setup hand is 4 cards.

Another scaling option is: add/reveal 1 more encounter card to the staging area during Scenario setup, depending on number of players.

3 players, add/reveal 1 more encounter card.
4 players, add/reveal 2 more encounter cards.

Another scaling option is increasing Initial Threat levels:

3 players, increase each player's starting threat level by 1 (or whatever amount will scale well).
4 players, increase each player's staring level by 2 (or whatever will scale well).

Mix and match the above to make the game scale better for more than 2 players.