To preface this post, I really like the shipwreck feature.
I think that the upgrades you get from the wrecks are too good. I do not think that you should ALWAYS get an exceptional upgrade from every wreck you find. I scavenged an Exceptional Powder Monkeys off of a trader's cutter, which is just absurd to me. Exceptional upgrades are meant to be rare - something to work for and extremely valuable and the current system makes all other upgrades Basic to Mastercraft irrelevant.
So my proposal is pretty simple (numbers can be tuned):
10% chance of Exceptional
15% chance of Mastercraft
75% chance of Fine
You are always guaranteed at least a Fine upgrade, however it is still possible to get lucky and get an Exceptional version. This allows people with 50 crafting to still be able to make some money off of upgrades, and provides a way for people lucky enough to get a bottle a chance of finding some good modules.
Reducing how frequently exceptional modules enter the game allow devs to increase the quantity of bottle drops. Now not every wreck you go to will have an exceptional upgrade, but you get more bottles to find more wrecks.