Ok, DMG, listen carefully.
If we played with no stages banned, how many stages would MK have a theoretical advantage on? Knowing his mechanics and the mechanics of Brawl, it's a likely supposition that (over-centralizing tactics aside), he'd have an advantage on a majority of stages. This is supported by the fact that he has a legitimate advantage on a majority of stages even after we ban the broken ones. We can suppose that, in the grand scheme, having stage advantages on a majority of stages is simply a part of MK being MK; it's as much a part of his mechanics as any of his moves.
Now, we have 3 choices when making a game system to play with:
* A system which artificially increase his advantages
* A system which artificially decreases his advantages
* A system which keep his advantages intact
An example of the first system is one which has Brinstar as a starter, while an example of the second would be a system which bans Brinstar altogether. However, I would ALSO argue that our current CP system does that, because we only allow a player to ban one stage per set, and MK, unlike other characters, has multiple amazing stages; MK has less to lose by having one of his stages banned from the set than another character. If we banned no stages per set, this would not be the case, because MK would (theoretically) always have his best CP available, but the opponent would as well (the relative gains per individual CP being irrelevant in this case, as they are an inherent part of each character, mechanically).
Now, look at the system I'm proposing. I argue that it is ACTUALLY the most fair, because of the inherent mechanics of striking. Let's assume, for the sake of argument, time, and the amount I have to type, that Brawl has 5 stages, all legal (A-E). It's MK versus Megaman. MK has 2 stages he's amazing on (A, B), one stage he's very good on (C), and 2 stages he's better than average on (D, E). Megaman, as the typical Brawler, has one stage he's amazing on (D), 1 stage he's better than average on (B), two stages he's average on (C, A), and one stage he's bad on (E).
MK will ban (in order) MM's best stage (D) and the stage he's better than average on (B).
MM will ban (in order) the stage MM is bad on (E) and one of MK's best stages (A).
This leaves them playing on stage C, a stage MK is very good on and a stage MM is average on. This is the most fair outcome, because the outlier stages are taken out and because MK has more stages he's good on, so he should get some sort of advantage.
If we have a system that either artificially increases OR reduces advantages (OR the number of advantageous positions), we are changing the balance of the game, many times without REASON (because of MK was worth changing the balance of the game, we'd just ban him). The system I'm proposing ALWAYS results in the least skewed results for stages, which give player skill the LARGEST amount of influence in the outcome of the match. Our current CP system allows for lesser skilled players to win a match by stage selection alone, whereas my proposed system negates that chance entirely by forcing (intelligent) players to fight on the least biased of stages for BOTH characters, but preserves the inherent advantages given to characters by their mechanics (not in intensity of advantages, but in number).