Any secondary is going to be worse than your main in terms of your skills and memorization and muscle memory. That's just the way it is. That means when you pick a secondary you will be worse than mains of that character. I'm not good with Sheik. Sheik is great, but people, everyone, knows the Sheik matchup. Even if I invested weeks and weeks into Sheik I'm not going to get results with her as a secondary. I really think the whole "high tier" secondary concept is horribly flawed. If you are gonna run a low tier main you have to run other low or mid tiers as secondaries. The reason being that people simply don't know the less common matchups that well, and even if they know it OK it's probably against a single playstyle for that character.
Basically, if you are running low or even a mid tier main that is unpopular you are using the knuckleball strategy. In baseball most of the best pitchers rely on their fastball. The exception is knuckleball pitchers. If you add another pitch to your lineup it shouldn't be a fastball (though hilariously in real life this is usually the other pitch knuckleball pitchers use, often to poor effect). You probably already tried that and established you don't have a great fastball. So you need to add another wacky pitch that's uncommon and hard to practice against.
What does that mean? Well, I'm waiting patiently for the MU chart to get finished. But that means you need to look at the MUs various mid and low tiers have and pick two (maybe three) that have an overall positive spread. I would suggest that Olimar is the top of what should be considered in popularity. Any more than that and the character gets enough exposure that lack of MU knowledge is harder to exploit.
Taking out the DLC aside from Mewtwo: here are the characters that you can viably exploit lack of MU knowledge. Keep in mind, the lower the usage, the worse the MU knowledge will be.
Pikmin & Olimar
554
Ike
549
Wario
547
Ganondorf
523
Lucario
517
Bowser
508
Falco
500
Pit
446
Jigglypuff
430
Palutena
420
Bowser Jr.
418
Robin
415
Mr. Game & Watch
411
Charizard
370
Samus
368
Pac-Man
367
Wii Fit Trainer
342
Duck Hunt
336
Lucina
286
Dr. Mario
230
Zelda
228
Dark Pit
203
Mii Brawler
182
Mewtwo
98
Mii Gunner
59
Mii Swordfighter
49
Ok, cool. So now you should pick out of those, characters that cover your bad MUs. I don't think it's by chance that I do better with Dr. Mario than Mario. Even if Mario is unarguably "better", everyone knows the MU. Not everyone knows the Doc matchup.
Zke99
to mitigate Fox, depending on local rules, Mii Brawler is a great option. I like Dr. Mario against him. Great tools for gimping Fox and I really don't think Fox has a good enough offstage game to capitalize on the Doc's weaknesses.