yea, if you want missions that take "teamwork" (meaning, an entire freaking fleet, ranging from fighters to battleships), they need to at least reward enough money to make them worthwhile.
A 400k, or even a 1 million credit mission, divided by the 4-5 players it takes to complete the mission, isnt even going to pay the repair bills.
NPC's are not meant to be equal to players, ever. That's why the spawn in groups of 4+. If NPC's spawn in a group of 4, they each need to be roughly 25% as strong as an equivalent player. That means 4 NPC fighters need to be balanced against ONE player fighter. 4 NPC destroyers need to be equivalent to 1 player cruiser. There's no other way to balance it which will make things relatively fair here.