I was worried that the game would be even more difficult with two than four particularly if we didn't get a good combination of roles. We drew the scientist and researcher roles which seemed like a fairly decent pairing and then started the game.
It seems counter intuitive, but the game is actually easier with fewer players. I would say that playing with 2 roles and 6 epidemics is actually easier than 4 roles and 4 epidemics.
Your pairing of scientist and researcher was probably the best pairing possible.
Great game for 2 players.