I am with you guys for scaling down the space station, but the ships are going to be a little more obvious. A half size cube would make the all of the other federation ships seem that much larger, and that kinda defeats the purpose.
In the end, the stations should be somewhere around the same size as each other (ergo, klingon space station and fed station should be about the same size, no matter what), otherwise you run into the problem that one races advantage is that it's stations will cover more grav well than others.
As for scaling back Cubes, they don't move when fighting and are supposed to be hulking behemoths, so size isn't all that big of an issue, just pop cap (perhaps make them more expensive both pop cap and resource wise, but with more attack, health, shields, e.t.c.).