Aerial Neutral B beats his entire move set except for hit boxes through the top and Fsmash (it doesn't cover his head, so high Neutral B will still beat everything). He can't directly kill you if you hit confirm>retreat to a platform if he shielded it.
My personal approach to the MU is dash in and stay out of his dash attack range and then poke at him until he tries to arrow and then Neutral B OoS after he arrows my shield because he can't set himself into a winning position from an arrow. He'll either shield/run away or he'll doing something else. The former will put you away from him and allow him to shoot arrows at you/force you to come back in and the latter puts him in juggle position. Poke safely once you're at kill percents and shield a lot because his throws are poor at killing/setting up for kills and his attacks either poke well and don't kill hardly at all or poke and are extremely obvious (he'll have to jump above you in order to Fair/Bair if you're at neutral).
Don't spot dodge if Pit is in the air (I don't really understand why people do this). If your shield is low and you're afraid to get Faired at high %, you're better off immediately reacting to his jump by rolling away (not into him). Dtilt/Ftilt/Shield mix-ups outside of his attack range pretty much shuts him down well. Pits jab frame traps on hit and can pseudo anti-air (I've seen Japanese Pits use it to beat low Dairs that would be other wise safe), but its hits box hits about as high as it does horizontally, and if you have a decent reaction time then you can stand outside of Pit's attack range and react to him dropping his shield with Ftilt (Dtilt hits low enough that you can whiff a Dtilt if you react to him jumping OoS, which will then allow him to punish). His fast options OoS are Usmash (frame 6) and shield drop>Utilt (frame 9), but these only really matter if you're Frolling into him/going for a cross-up/trying to be inside of him for any reason. His threating OoS options are jump/Up-B>Dair (5+10 frames=15 [if Ftilt/Dtilt isn't well-spaced on Pit's shield, this will hit MK's hand]) and jump/Up-B>Fair (5+12=17) if you're camping high in the air (generally not a good idea bceause it gives Pit a lot more flexibility in his keep away game).
He also has drop shield>Jab (7+5=12), which is respectable considering the frame trap that I mentioned earlier. Basically, it gives Pit enough of an advantage that he jab and then grab if you shield (or if you attempt ti Ftilt/Dtilt, depending on the %), and Dsmash/Stutter-step Fsmash option-select your spot dodge/Froll and dash attack either roll away. Furthermore, his Fsmash is only a frame slower and covers a little more horizontal distance. It also happens to be slightly weaker than MK's Dsmash. If you're buffering your frame traps or your opponent is reacting to anything other than Ftilt 3 then Fsmash isn't an issue.
The reason that spacing is important is that buffered MK's Dtilt>anything but shield/spot dodge or MK's Ftilt>anything but Ftilt 2 will be interrupted by Pit's Fsmash OoS and Pit's jab OoS is guaranteed on anything other than frame perfect Dtilt>Shield. Fortunately however, these all require reads and jab's kill follow ups require a second read.
If Pit is gliding back to the stage then you should either Up-B with a read, bait the glide attack so that the momentum carries him into you (e.g. putting yourself an Up-B position and Uair/Nairing instead). Pretty much only Neutral B will consistently beat it (unless Pit will be hitting cleanly through the top). Glide attack easily out-ranges pretty much every attack that MK has, including MK's glide attack (outside of a few uncommon spacings where MK's glide attack is above Pit's, similar to how MK's glide attack can beat itself).
If MK is standing/able to act at neutral and the opponent tries to jump above the stage while recovering (a.k.a. doesn't know the MU), feel free to Up-B him for free kills if Pit has used up his glide. Otori Up-Bs are great if the opponent doesn't know how to deal with it (very few people seem to know how). Reacting to Pit's jumps when MK is at low % is good (you're better off playing safely after ~90%, because Pit can bait the Up-B and trade with Bair, which is very strong). Try not to be greedy if Pit is being greedy with Bair fishing and just run away/take safe pokes at him when he is. Retreating Fair is good (loses to well- timed/spaced dash attack) and the classic retreating FFFair>Dtilt is good in general.
You can't grab his Ftilt/Dtilt if they have any decent spacing, but Up-B OoS/Ftilt OoS are easy fix-alls for punishing him touching your shield. Pit's arrow can be safe on block unless MK is close and a lot of Pits get their damage/kills from spot dodging what looked to be an unsafe arrow and then punishing a whiff with Fsmash.
Another mid-screen approach is to read arrow>arrow (it can be pretty easy to read when you aren't close to Pit) and power shield the first arrow>dash attack to clash with the second arrow. This will generally result in MK being in one of three situations: Covering ground without taking damage (Pit will have a significant frame advantage but won't be close enough to do anything about it); MK will be close enough that Pit can punish and will have clashed late enough that Pit still has a frame advantage; MK will clash with the arrow shortly after Pit fired it and will put MK near Pit allowing for significant punish (Up-B/Dsmash/dash grab/Ftilt/etc.). The second possibility is the least likely to occur, fortunately for MK. Ftilt is a given, however this can occasionally lead to free second hit Dsmashes for relatively early kills.
Whoever gets the first kill will have a significant advantage in the MU, as both characters can run away from each other and tack on a lot of free damage (MK more so than Pit, however a frustrated MK player will often lose most -- if not the remainder -- of his next stock).
I'm sure that I'm forgetting a lot since this is all off of the top of my head, but basic MK should remember the following:
- Neutral B totally beats Pit in the air.
- Spaced Ftilt/Dtilt/Shield mix-ups dominates Pit on the ground and Neutral B is good here as well.
- As per usual, approaching with Neutral B is not a good idea; Pit can throw you right back out with arrow follow-ups to rack up damage very quickly, and without adding in shield damage that allows it to eventually poke.
- Pay attention to how you recover because he can randomly Down-B your Side-B/Up-B/Neutral B. Down-B recoveries are pretty good.
