It all depends entirely on how the ships are used in a mission. After all, ships don't exist in a void. Substituting a Lilith for a Cain, or changing the angle the Sobek warps in at, can have huge impacts on the way the mission plays. I would recommend trial and error testing to see if things work the way you like. Even in multiplayer, this is the way you find out.
Here's a rule of thumb: if you find yourself always wanting to use one particular fighter, or weapon, and never using certain ones, then they're probably out of balance. Adjust things until the strengths and weaknesses balance each other out.