You can power up the weapons, you can randomly buff skill tree points, but you can't make up for the fact they have 2 forward weapons and 1 aft weapon. You can't make up for the fact they only have 4 boff skills on their ship (IF that many).
Had somebody in a tier1 connie in an elite STF. Doesn't matter if they had MACO shields, and thought they were having a blast... Truth is the team suffered for their lack of firepower, and the rest of us carried that ship. Not saying the player wasn't skilled, but it's the equivelant of carrying somebody on ground STFs that has a mk.0 shield and default free phaser pistol.
Some things don't scale. Instead, scale DOWN the enemy level to match. That scales rather well.