If really something have to say about the difficulty of encounters, it is about the "learning curve" requested to the player: jumping from a no brainer tank and spank, to something that require collaboration of full group, is an huge gap, and I think the Main Scenario needs help the player to learn that, with some progression.
Starting from tank and spank, and with progression into the story, new duties will need to require new player's abilities a little at time, so when the player comes to a full collaboration duty, it is just something little added to previous duties he already learnt. So, it will be a story progression that goes hand in hand with player's progression.
If, instead, the Main story is really intended "for all", it is needed to avoid this kind of difficulty on the Main Scenario, at all.
The player who will enjoy improving himself will then need to have alternatives. I just can think of some sort of "Main Scenario (Hard)" quest chain, but it is clearly out the options as far as we are with the game. I'm sure devs can go up with better ideas. Those are my thoughts about the overall issue of hard to clear Main Scenario duties.