MK is banned in my ruleset, yes, however all of those stages are still viable with MK legal.
He already gets to choose between RC or Brinstar, so what's the issue? DP (with LGL) isn't even that good for him, nor is PTAD (He can't shark or plank).
I use the larger stagelist with two stage bans in both singles AND doubles, and it works great, I encourage you to at least try it out, if only as a side event.
The game is a lot deeper with more stages.
My first point is going to be that out here we don't actually play with RC legal, when I included it before I was assuming RC would be legal in your ruleset because stages like PTAD and Norfair are legal in your stagelist.
I never said Distant Planet was good for MK anyway, so it's irrelevant.
PTAD however is good for MK. MK can recover just as well here because of his insane recovery options, he has no need for ledges. 90% of the cast do though. His gimping potential is going to be amazing, and just because you can use the floor to bounce yourself back up doesn't mean his gimping is hurt at all. If he follows your DI on the floor bounce properly, you're taking extra damage, again, again and again. And if we consider the cars on this stage that kill ridiculously low, (about 40-50 I believe) the viability of this stage goes down the drain. I can understand points about how 'it helps people with poor kill options', but it also helps people with already good kill options. It might be different if they were a little weaker and killed at about 80 or so, but the strength on the cars is too great to be considered an acceptable hazard regardless of their predictability. They also promote small moments in which camping is required due to the inability to approach through the cars.
I think it's rather naive to assume that a stage isn't good for MK just because he can't plank or shark. MK is the best for many more reasons than his inpenetrable planking game.
That aside, including the two bans rule in singles is interesting if it gives more viability to more stages, but I think that you should still tweak your stagelist just a little so that there's only 3 of those 'mk broken' stages (again for example, I'm thinking of MK).
By that I mean to say out of RC, Brinstar, PTAD and Norfair, only 3 of these are legal. In this instance, MK will get a counterpick, but nothing that's too broken against every character in the game. By choosing only 3 of the above stages (I have RC, Brinstar and Norfair in mind) every character will have a stage that is at the very least 'winnable' against MK. Again, assuming you have a LGL.
Also, assuming an MK get's far enough in bracket to play best of 5 sets (which he will obviously) he only get's one of those above stages, and another CP such as Lylat Cruise or another stage dependant on the opponents character.
I'm just thinking out loud though, if there's an obvious flaw in my logic tell me about it.