I definitely feel that something is off on these missions. When you have the frigate hull, and even the destroyer hull, the missions always feel so difficult, like you are using a pistol to take out a tank. Later once you've unlocked the later hulls, you've got the upgrades and modules such that now you can steam roll every other mission it throws at you. It's like the difficulty is very high early on, but drops off sharply at some point rather than the other way around.
The final missions I was just sending my ship in directly to wipe out the large bases and all the small bases in sequence without pause. Nothing could really stop me if I used my shadow shield at the right time. Heck, I didn't stop for defending any of the allied bases and nothing went down at all. The last mission branched off an AI Homeworld so getting to was actually harder than the mission itself.
Just an aside, the build I was using for my champion was: Zenith shadow ship, 1-2 shields of the highest mark, 1-2 bomber bays of the highest mark, 1-2 interceptor bays of the highest mark, and MK2 MLRS and Laser turrets. The combined firepower plus the fact that the stations loved splitting their fire to my spawns meant I was able to push them over before they could get me.