The Naboo have their ships of state.
The running gag could be that while they look lovely they always get shot down or blown up (the red shirt ships of the new PT).
When forced to land on Tatooine, the Royal Yacht is damaged and maybe Watto has a funky looking ship which is a good ship but still more expensive than trading in the badly damaged Royal Yacht (this is what Anakin races for, the extra money).
Perhaps it could be used instead of the refugee ship in AOTC too (the galley scene could be given a different background to make it like those scenes in the Falcon when people are sitting back, playing chess or musing on dead knights).
As a Senator Padme still has to use the Naboo ships on state visits but when she travels to Tatooine she could take the funky ship (her own personal property) and when she tries to find her husband the funky ship flies one last time.
Anakin could have added interesting modifications to it over the years but it could also be a place where Padme could let her hair down (literally considering what George likes to do with it).
I see what you mean about mirroring the OT but on the flip side I thought the PT seemed to skewed towards putting as many toys out as possible, no central villain, no central ship because each new thing could be sold as a new toy.
This led to a world which there is no sense of growing attachment to the objects and characters contained in it.
Threepio and Boba Fett on the other hand are given bizarre origins and very little to do which is consistent with their defined roles. They are only there to carry them over to the OT with very little thought given to what they are doing (as dumb fan service goes having Vader build the Falcon makes more sense than having him build Threepio so he can act like a twit for two films and have his memory erased in the third after doing hardly anything).