Just reading the initial idea, and thought I would pitch in my own two cents...
Essentially, I approve of upgrades, side-grades and asymmetrical ships, although, I do not think ships should be allowed to swap out entirely different classes of weapons. Taking the Human Cruiser example, you should be able to upgrade different components of it (better thrusters/turn and burners, modified missiles, modified lasers, more armor/crew, better shields etc.) and maybe even have some unique upgrades for each ship (human ships, for example, could have a potential upgrade which makes their armor and shields 50% more effective against "projectile weapons" while making it 10% weaker against biological, laser, plasma etc.). But I do not think you should be able to exchange completely different weapons on ships, otherwise that would make many ships obsolete as why would you ever use an Earthling Cruiser (or an Earthling Destroyer, if there is any push to have multiple ships per race, as seen in Star Control Time Warp) when there are other ships that are faster, stronger and can mount the same or very similar missiles that you have? Essentially, I think your ships should have micro-upgrades or even 1-3 different weapon options per primary and auxiliary, but I also think we should be cautious about having weapons overlap on these ships, as if they did it is likely we would all just be using the same ship "chassis" that turns out to be the best mix of fast and durable, and just strapping on whatever weapons we see fit onto it.
Alternatively, if for whatever reason we did want to go ahead with overlapping weapons is that we could say that a Earthling Cruiser can use the Missile Mk. I, Mk. II, Mk. III and Mk. IV (hopefully they wouldn't be named such, and would be unique from one another, like having a cluster missile instead of a nuclear warhead or such) but if you wanted to mount the Earthling Cruiser's missiles on Alien Ship Y, you would be restricted to only the Mk. I variant of those nuclear missiles (so no cluster munitions for you!). This would help balance the desire to only use the most powerful chassis, while also giving some unique weapon diversity to these ships (think spammy Earthling Cruiser with Supox goo cannon, or whatever equivalent there would be to that in game, imagine the potential!)
Those are just my thoughts, and it may turn out that I am in the minority, but I would love to hear your thoughts.