I think honestly, whatever we decide on, there's going to be an "optimized" way of doing it, but I also think that cut and past-y ships won't be a problem unless everyone starts suddenly just trying to maximize their weapons all the time.
As to your suggestion Wes, I'm not sure what benefit or consequence that would have. I think it would mostly just shift the 'optimum way' from 1 +2, 1+1 and lots of little ones, to 1+2, 3 on tier, and lots of other ones. Whether that's better or worse, I'm not really sure.