Even if certain builds become easier or harder to spec for, a few skill points here or there isn't going to majorly change balance. It does look like you can apply more passive bonuses to your ship, but that's true for all three classes.
All I can say about what we have seen at this point is, if you thought this was Star Turtles Online before, you ain't seen nothing yet. Just take a glance at their "draft / early version / in no way final / probably nowhere near as f'ed up as it will be by the time we finally roll it out" skill tree that Gecko posted: all the healamatic skills in T1/2; all the DPS skills in T4/5. Yum.