There are all sorts of factors that I'm guessing Frontier considered when making ships; jump range, speed, pitch/roll/yaw rates, cargo capacity, weapons, utility slots, running heat, hull, hardness, shield values, potential unlock, etc. I'd wager if something was made really good at one thing, it paid for it by getting hit in another area.
Every ship can't have the best of everything or they would all be the same thing. The game has changed a bit too, so some of the stuff that maybe mattered back when they designed some of these ships (price comes to mind) are all but irrelevant now, so any trade offs a ship might have taken to be good at one thing just might not make a lot of sense in the current state of the game.
Yes, a Courier with max size shields will have more shields than a Clipper with max size shields. Why shouldn't it be that way? Why should a Clipper innately deserve a higher shield value when using max size shields than a Courier?