I think there is a bit of a problem with the STF missions. A lot of people will agree that the invisible borg torps are just overpowered. That is something like what I'm going to be getting in to, but not just that.
I feel like, at least for the pre-50 level characters, Mirror Invasion is a really fun mission. Fighting larger amounts of average difficulty ships and then having a boss(Stadi) at the end was fun. The enemy ships fire constantly with average attacks. The damage can be overwhelming and kill people, but there was at least some back and forth. There was healing, picking proper targets, using AoE abilities etc... Stadi itself was fun because it was challenging, but not overpowered. His apparent combination of Beam Overload and Beam Fire At Will hurt, as does the torp skills. There were ways to counter and survive it. However... this is not what we can expect from STF missions.
For some reason, the STF missions were designed in a way that the enemy ships would rarely attack, but when they did... it was almost always one shot. On my Fleet Advanced Heavy Cruiser Retrofit I have 58k hull. I use 1 Neutronium Alloy and 3 Monotanium Alloy eng consoles. Even with full shields and hull, I get hit by a sphere for ~20-30k hull damage in elite. With 52-59% Kinetic resist, that shouldn't really happen. I know there are diminishing returns on consoles, but it is still more than not having them at all. I understand that Elite STF missions are supposed to be difficult, but I don't think raising damage on enemy attacks is the only way to go. I think their damage should be reduced and have their rate of fire increased. One shot = not fun. That brings up another point... Borg use plasma torpedoes. Plasma torps should be relatively low impact damage, they aren't quantums or photon torps. They are used for the Plasma DoT -after- the impact. They shouldn't do crazy impact damage -and- crazy DoT too. If one had to be chosen, it should be the one that the weapon was meant to be for, the DoT, which in my opinion is where it should be for elites.
I just feel like back and forth combat is more fair/enjoyable than taking no damage for a while and then immediately one shot. This is not even including the fact that borg love to shoot invisible torps. The game is heavily DPS based as is. Yes, some people claim their support ships are awesome, which can help, but usually not as much as another high DPS ship in STF missions. Making the battles more balanced with damage can make it more enjoyable and open up more options for support builds. Just to be clear, I'm not saying lower the DPS of the enemy ships, I'm saying nerf them the way that tricobalts were nerfed. Fire faster but less damage per hit.