Then it's not size but some "damage potential" metric. Where does an imperial courier fit? it's got shields about as good as a vulture and if you fit it with three medium rails it can do about as much damage. Is python still considered medium if it's stock and only fitted with two small pulse lasers?
If you got into that much detail it would be too complicated to work. Originally I thought it should be a points system with each ship having a different value, similar to how a board game would work it. That's too cumbersome to apply to a video game though, so it has to be simplified. The outfitting of the ship can't come into it, or you end up bogging things down in some sort of wing wide spreadsheet.
The point of the entire thing is that a vertical progression coupled with a flat wing size will eventually result in wings of all Anacondas if PvP combat becomes the norm. It's essential that they do a balancing pass not only on the ship's themselves but also on the wing system.
The most important part is taking a look at the vertical progression model and giving smaller ships a role to fill.