I don't think that putting a hard buff on ship classes is the way to go. One of the things I like about this game is that you can get different results from different ship/captain mixes. So, instead of just three classes, you have nine different combinations, each with different results.
However, I do think that Tactical officers Attack Pattern Alpha needs to be applied specifically to weapons power. This is why a Tactical officer can take a grav well and make it deadly. If you remove that specific buff, then the super powered Tac/Sci boat is not as viable of an option. Everything else after this I believe will start balancing out.