usage rate is a reasonable way to allocate between freight and colony, but liners are going to present some problems. they have zero idle time, ever, and while you're confined to one system (with very short transit times) their ROE is sky high. weight by usage or profit and you're going to wind up with a lot of liners and a lot of wealth production. which is actually *correct* given the economics of aurora, but amounts to an exploit since the economics are so underdeveloped.
i imagine you'd see similar behavior vis a vis colony ships for players who use the infinite wealth earth-moon round trip exploit.
would it be so bad just to let the player decide which types of ships subsidy funds are spent on? make the "profits squandered" portion a bit higher, and call it a day? youd have to have the designs published before the first one is built, but among other things players can keep the population of small civ units down, which is good in a lot of ways.
the other approach is just an elaboration of StHM's one: you take the time to make sure you have shipping profits (in particular ROE) really right, and keep track of annual ROE by ship class. have newer (and larger!) designs assigned tasks preferentially, and where ROE is high you build new ships and where ROE is low you retire. this is a lot more work and i am not requesting you spend the time... but dare i say it is in the spirit of how aurora is developed and played? OCD is an ugly disease