I still believe that this would be a good idea, especially since cruisers and even battleships are allowed to shoot transports under the correct circumstances. This would allow transports to survive even a Battleship Heavy Mortar round. While yes, a transport attempting to engage a battleship would be doomed in a 1v1 scenario anyways, it would still prevent a one-shot kill, and allow even PvP rookies who don't fly anything but transports to make more of a difference in a group fight.
In a less extreme scenario, a Cruiser Light Mortar to a transport's hull would very likely grab someone's attention enough to get the transport pilot to potentially be less flighty. This I feel is a lot better than say, a rookie player sporting a generic AU seeing 70-90% of their hull melt before their eyes, panicking, then choosing to run.
Again, as a pirate I wouldn't want to one shot a transport with a SNAC, or LM, or any other big weapon. Yes, an EMP+SNAC bomber is terrible for piracy, but that doesn't seem to stop some folks from trying, especially if they're simply passing through an area and suddenly, "Oh look, a transport!" As a policeman, I also would not wish to one-shot a smuggler's hull simply because I forgot to check and see that they don't actually have an armor upgrade.
As a side note, maybe simply bumping every transport in the game's cargo up 20 units would be a good compromise. Something needs to be done, in my opinion. Having to forsake both armor and good shielding in order to supply PoBs optimally feels like overkill.
But I still think merging nanos into the hull would be nifty, especially since suddenly Repair Ships would be excellent escort assets due to how their Repair Tools function. As transports have been one of my most flown ship types recently for RP purposes (PelicanPelicanPelicanPelican), I would love to see this happen.
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