I kind of skimmed past the big posts. Just on a brief note: Pierce, you shouldn't have to call on others to back yourself up. You sound less of an authoritative figure on the subject and more of a ***** riding on the backs of others when you do that, regardless of right or wrong. My 2 cents.
Anyway, tid bits on the MK MU I guess others should know:
Jab sucks. Long as you actually recognize the animation/sound and are familiar with the start-up, you should be able to know when you can punish and when you should just keep shielding as the MK is bound to pull out a move.
F-tilt has more lag on the second and third than the first. Someone has already mentioned the frame data so I won't go into specifics. Understanding the spacing required and that an MK normally has to walk to use this as a poking manuever could set your character up for multiple approaches. Dash in shield for example.
*Please bear in mind, I'm not theorycrafting, I'm simply stating your options. Obviously, the MK doesn't just have f-tilt as his option.*
D-tilt is safe on block when spaced but never safe on hit at low percents. Most characters with a frame 6 move or faster can punish d-tilt until perhaps around 50%? Around the time d-tilt has significant knockback that you're not in range to punish. So if MK attempts to use d-tilt as a poke maneuver, just know you can always play the gambit and let it connect just so you can punish. Just be careful. I never understood this, but if you crouch you're even more prone to trip to moves that have a potential of tripping. I tend to fall into this whenever I try punishing with my d-tilt instead of my jab on occasion.
U-tilt has superb range and a long lasting hitbox. You can't exactly land next to an MK in other words. For that matter, MK could always frame trap a u-air->n-air instead as well. Best advice is to take advantage of MK's aerial immobility and go for the ledge.
F-smash... well it's slow. That's the only negative side of that move. It's pretty safe on shield, kind of risky to attempt to perfect shield it.
D-smash, as someone mentioned earlier, has a lot of cooldown, both front and back. Learning what your characters options are and ingraining into yourself the proper response can really get you far in this MU.
U-smash is underused so I won't discuss it.
U-air is a godsend for MK. If your character has a move that has greater range than u-air, lucky you (Lucario, Wolf, etc.) Otherwise, again, take advantage of the aerial immobility.
D-air has significant lag at the end of it. Characters such as Sheik, ZSS and Falco have easy answers to d-air due to their high first jump and fast double jumps. Any characters with projectiles also tend to have better answers to d-air. On stages such as BF and SV, try to position yourself as close as possible using the ledges before attempting to chase MK. As someone noted earlier, crouching also helps in this case.
F-air... I still haven't gotten the hang of it, but you can always SDI up out of f-air on reaction if you train yourself to react that way. Meaning the higher the percent, the less likely f-air can ever be used as a juggler or kill move. Full-hop f-air is safe on a lot of characters though, however, MK is also in the air so depending on his follow-up option, you can still punish if you shielded the f-air.
B-air... is gay. The set-ups it provides are hilarious whenever I see them. Your best option is to SDI up (and footstool if they cancel the b-air.)
What else?
Tornado is punishable by any strong, disjointed hitbox. It doesn't have to be heavily disjointed however. IE., Samus can f-smash tilted up a tornado. This doesn't necessarily work the higher the tornado is (which for me example, has to be significantly high.)
Crouching again comes into play. The likelihood of perfect shielding is better. However, it would be wise to have an option that covers both sides, considering that if he's nadoin' that high, he can probably lagless land it. In other words, instead of going for the grab or tilt, it would be wiser to go for the aerial, as most d-airs or n-airs cover both sides. Even up+b works (my personal options.) Doesn't really apply to certain characters obviously.
In order for nado to trap you in, they have to slow their pace as soon as they hit you. A perfectly executed nado is something you can't really escape. SDI does not apply. Luckily, not everyone knows how to do this. Thus, if you get knocked out, your options differ depending on how you get out.
If you got knocked up, most characters have an aerial that can break nado. I still see Falco's attempt to d-air, or Lucario's attempt to d-air. These are the wrong choices if you ever get out. Use the right ones (n-air in both examples.) If you just fall out, air dodge into shield. Depending on your fall speed and how far you are from the ground, it could be a highly favorable position or you just get hit by last hitbox of nado. =/
Kind of tired now. I would go over how you can abuse the recoveries of MKs and stuff on gliding, but I'm sure someone is bound to argue over some point I made. "That's theorycraft" or "MK can do this."
Look. My experience speaks for itself. Take it from a low tier who's learned the ins and outs of MK as a character. If you really want more help in the MU, regardless of your character, you can contact in some form that isn't smashboards.