I have often thought that limiting big ships from docking at small bases was a good idea, and I like Sovereign aerodynamical argument. It kinda throws a spanner into the mix and complicates the matter, but I like it never the less. I do think it would reduce Cap-usage and this has nothing to do with game balance as another pointed out. Now if we were to restrict capships saying they couldn't use trade lanes - another idea I'm fond of - I could well imagine criticism mounting up.
One thing though - certain restructuring would need to take place e.g. you could buy a Pirate Cruiser at Bornholm, but you couldnt dock with one.