Hero Ship upgrades

That is a good idea for keeping the scalability.  

The inherent problem with the Hero ships, of course, is they are small hulls.  Military ships throughout their lifetime and in the game can be upgraded and retrofitted, howver the hull stays the same. Most of the hulls allow for enough modules to protect the hero ship enough like the adamantium jammer.  The Guardian - Tamad ship is the exception to that.   I don't think the others need too many more modules for the small hull, because of space constraints. I feel most of the hero ships are well balanced for their purpose.  However, Armor is the exception, because armor technically goes to the outside of the ship and it is really no big deal to add more with the technological advances.  

As long as they have 3 module slots, and double armor I am good with that. The armor technically would also serve a hull upgrade.

Ultimately, I didn't want it to feel like it was cheating in an unrealistic manner, and that is the main reason that weapons would be unchanged.

I do think the resources would be a great idea, and you could be charged as a resource slot for them as well.  Without bigger hulls, this was the best way I could think of to help them out late game.