They will have no choice. It's simply not possible to balance a game as big as this perfectly to the point that every ship and combination of ships will always be equally competitive.
There will always be a best list, and there will always be a worst list. There will always be combinations of ships and upgrades that go well together, and combinations that don't.
The hope is that what's on top and what's at the bottom will not get as far apart as they did in 1e, and that they will be changed more regularly and with more fine control.