But to keep the ship balanced it would have to be just OK in all three areas. Sure I could have a ship that gave me equal access to my engineering, science, and tactical BOff abilities. But it couldn't be as good as any of the other ships are individually of the same level, or no one would play specialist ships. What would end up happening is that you have a ship that either everyone played because it was superior to all other ships, or a ship no one would play since it didn't allow the higher level abilities that the other ships allowed.
I'd love to see more variety in ships, and less of an emphasis on science career people flying science ships. A ship whose premise is "balance" is a cool thought.
Honestly, my best character is a Tactical officer who pilots a Science vessel. He is skill loaded in star ship operations to improve the BOffs. As far as I can tell most of the profession specific skills have little effect on space combat and more effect on ground.