Title says it all really. If this is a game where you build your fleet, you should have meaningful choices when doing so. You should get to pick if you want shrouds or cartouches, but the problem is that a lot of the lists waste a huge amount of points when doing so, as a lot of the lists not only have no ship under 50 points, which is a LOT in a 2v2 list of 600, but also are subject to design restrictions like escort limits, that might prevent you from even buying a 50 point ship.
In order to improve flexibility in list design, I think there should be something similar to total war: warhammer: a veterancy system. In total war: warhammer, troops in multiplayer don't have persistent experience. At the start of each match, after building your list, you just spend your extra points buying "chevrons" for troops, which just makes them generically better. Better morale, better weapon skill, better defense skill. This is not designed to be super powerful. It's not typical in the meta to give all your troops chevrons, or even any of your troops max chevrons. But it allows spare points to not be worthless.
This performs a very important function for allowing someone to build a list and still get value out of half a unit's worth of points left at the end. And BFG armada 2 desperately needs this. It feels terrible to submit a list that is 570 points, but if you don't want to do that, often you have few if any meaningful choices about what your list consists of. There just aren't many combinations of scythe harvesters and jackals that let you decide what your want your list to BE or DO.
TLDR: let players spend points at the end of multiplayer list creation on upgrading units slightly, for small amounts of points, to remove the incentive to just pick whatever ships add up to as close to 600 or 1200 points as possible, and allow them to actually choose the ships they want.