I understand what you mean. But at the end of the day, the best students get the best results. The differences between exam boards, as (for example) the style of questions suiting certain people, it's only going to create a few mark difference. And no University or Sixth Form decides a place based on a few marks, so these disparities are almost useless.
Before you get to University, none of the content is particularly challenging, just lengthy. Changing an exam board will not improve your grades, you will still achieve a top top grade if you're a top student.
Also, for example, I sat an A2 module at AS level for one of my maths qualifications, whereas most schools sit one of the easier AS modules. I still don't see that as unfair, as Universities can see the modules we're taking. They're able to account for the differences. Plus, I've never met anywhere that takes GCSE's particularly seriously beyond the general "you must've not failed".
I just think that the difference in your score if you were to take the "best exam board for you" (if that even exists) would be so insignificant it's hardly worth the debate.
Nobody is ever a couple marks off their target for a reason (outside the extremes of course) that could not have been solved by trying harder.