I can't pretend to know all of Pika's MU so I'll just talk about the ones I know well.
ROY (-3): I really agree with you Psyant, about the Roy MU. He has all of Marth's spacing tools, but unlike Marth, you can't simply walk in his sword to avoid the tipper, instead you'll be walking directly in his sweet spot! I find it awfully difficult to recover against an opponent who would simply stand on the ledge spamming either neutral B or fsmash. Miss the sweet spot and you're dead. Try to go above or through them and more often then not it will kill you. Roy really forces Pika to have a perfect recovery, plus he has a crazy good neutral game against him. The only bright side is that once you catch him good, he's total combo food, and pretty easy to edgeguard if you have the tech skills for it. Overall, though, I'd say it's one of Pika's worst MUs.
BOWSER (-2): Bowser is a very hard MU for Pika because of his CC. It pretty much renders all of Pika's approaches useless, and moves that would normally start combos like utilt and rising uair won't work most of the time. Bowser being an incredible tank, usmash doesn't kill him easily. You gotta abuse grabs to keep him from taking too much advantage of his CC. Bowser can be tricky to edgeguard, since his up B beats Pika's nair, and he moves so far horizontally.
MR GAME & WATCH (-2): Another MU that is bad for Pika almost entirely because of CC. G&W can simply CC everything Pika throws at him and dtilt, and he has good follow ups on his throws. That same dtilt is also probably the best edgeguarding tool there is against Pika. G&W can cover the ledge easily to prevent Pika from sweet spotting, which makes recovering pretty tricky. Pika does have good combos on G&W, but I've always struggled to sneak in that early usmash or that surprise bair to close off stocks.
LUIGI (-1): This MU is a bit weird. Luigi does have a slight advantage against Pika, mainly because of his hit recovery. He can often break your uair chains with his nair, which can kill at pretty low percentages on small stages. Both characters have a great ground game, which makes for some interesting spacing, but overall I think Luigi's is a bit better. Luigi being Luigi, he's also pretty much the only character even Pika struggles to edgeguard. On the other hand, usmash will kill at crazy low percentages on all stages except the biggest ones, especially if you snipe them with down B.
GANONDORF (-1): Ganon hits like a train and has good range on most of his moves. He has good chain grabs on Pika, and his ftilt is a scary spacing tool. On the other hand, Ganondorf can't edgeguard Pika in his craziest dreams, but Pika has a complete tool set to dispose of him. Learning to snipe people with neutral B is very useful.
FALCON (+1): Falcon has a great punish game and hits like a truck if you get knee'd, but if you live past a certain threshold, you'll live forever. He has one of the worst recoveries. Simply taking advantage of that makes the MU much easier.
LINK (+1): I think this MU is pretty even overall, with both characters having good combos on each other. Pika can simply go through Link's boomerang or arrows with a nair, which makes it difficult for Link to maintain his space. Most of Pika's tilts come out faster than Link's and dthrow into usmash can kill at certain percentages. Because Pika's spark follows the stage, it's really dangerous for Link to use his tether, especially on walled stages.
ZELDA (+2): Zelda is a charm to play against. Pika can simply overwhelm her with a flurry of little hits and juggle her for days at low percentages. Usmash kills at very low percentages, and Pika's speed and mobility make it very hard for Zelda to use her projectile at all. Plus, nair beats her side B, so it's not even that threatening. Her recovery is also very easy to predict, which makes edgeguarding pretty easy. If you can force her to recover on the stage from far away enough, she'll have enough landing lag on her up B for you to do pretty much anything you want.
Ivysaur, Squirtle, Lucario, Marth, Ike, DK, Sonic, Kirby and Dedede are all pretty even MUs in my opinion. The others, I don't know them well enough to give a good estimate.
