Scaling ships smaller does not have to be a negative due to grav well transverse time. You can easily make speeds double, increase mass and speed up time so they may take a few seconds to get to speed but once they do, zoom zoom zoom. I suggested this in SoA, and to have structures meant to help speed in friendly wells so you can build "Speed Path Highways" or something.
mephistopheles
It's not just a matter of trversal time but also a matter of space to manage. Actually finding the attacking enemy fleet would be a timeconsuming if even feasible endeavor on any realistic scale. STatic defenses would become even worse due to the increased scale of a gravity well.
not to mention to actually move between a galaxy view and a scale where you can actually manage combat players would have to do entirely too much camera work.
The game just wouldn't flow as well as it does now. When it comes down to it, realism is all good and fine, but generally isn't advisable when it comes at the expense of gameplay.