Sonic is definitely not a bad MU for Mega Man, I don't think he gets any worse than even to be honest, with or without customs. His speed top notch and he can combo for days, but he has a linear approach and can't do much about lemons. None of his aerials are safe on block, homing attack has low priority and gets beat out by Usmash, spindash also has low priority and is hard to use in this matchup because of lemons and leaf shield. He does have many options out of his spindash and has many ways to mic up his approach, but none of them are particularly safe and he's almost always putting himself at risk when approaching. He has to play a heavy bait and punish game an Sonic in general can't really deal with characters good at zoning, constantly punishing you and avoiding being punished. If you play it safe and don't make enough mistakes that he can punish, I feel its slightly in our favor. Also, his landing options SUCK and he's screwed if opponents are directly below him. Anytime you catch Sonic airborne do everything you can to nab him with Air Shooter or Charge Shot if he does Spring > Dair, he's gonna hate those moves. Not an easy matchup by any means, but I do think we win it.
Just a few days ago, I faced the best Sonic in my state (who is considered by many of us to be a PR contender and he got 3rd place in this particular tournament, while I got 2nd) 2 times in bracket and I ended up winning both times. He had quite a hard time getting past my lemons and there weren't too many opportunists where he got to use his spindash combos against me as long as I made good lemon usage and leaf shields, and he really hated the Uair. I beat him 2-0 the first time in winner's finals and 3-2 in loser's finals. After game 1 in both sets he adapted fairly well and did much better than before but in the end I still prevailed. I do think I outplayed him a bit though and he admitted so, mostly because I felt he was fishing for kills a bit too much with his smash (speaking of kills, another thing worth mentioning is that while his kill moves aren't bad, he doesn't really have any guaranteed kill setups) attacks and he SD'd on his recovery at least twice. Other than that tho, everyone makes mistakes, and I felt that was otherwise a good feel for the matchup.