So
Thor
these are my thoughts on the MK matchup.
Punish Game - This aspect of the match-up MK has a +1 advantage in simply because of his silly kill strings. Pika does get very strong strings and combos on him due to his fall speed and weight however, so getting touched matters a lot in this match-up.
Neutral - Pika has a +2 advantage in neutral pretty easily. Even with the new shield mechanics, and his great aerial frame data, I think MK should be scared to try and jump in on Pika. Pika's ability to maintain and take stage position is just greater than MK. AC dair and fair are better zoning tools than anything in MK's kit, and he has no real answer to t-jolt. Sure MK bair, fair and nair all are pretty good anti QA tools, but they really require a read on the MKs part. Overall this is a matchup where pika is at advantage from mid and far spacings. I think MK's frame data and itty bitty disjoint gives him a slight advantage in super close range, but it's nowhere near as annoying disadvantaged as the Luigi matchup.
Offstage - MK +.5 here. I think his edge gaurding is more potent than pika, and even though his recovery is more linear than ours, you gotta love the multiple jumps. Also shuttle loop should scare anyone who tries to edgegaurd him.
How stage picks effect this matchup is a little bit of a mystery to me. There isn't really a legal stage where pika really has to be more afraid of MK than any other, I say CP to your comfort.
I think pika's advantage in neutral over MK is more easily converted to a win than MK's slight punish and offstage advantages. With QA to get away, we simply don't really have to play MK's footsie and bait and punish game. The MK player can't afford to drop any punishes or to concede positional or life/stock advantages. The pika player can do both those things and still have a good shot at winning.