Generally speaking, the best way to counter your bad matchups is to just learn a utility character, someone with very few bad matchups. Raiden and Kabal are the absolute best utility characters, IMO, because they hardly have any matchups worse than 5-5 (Reptile is arguably 6-4 with Raiden and I've heard Kitana is 6-4 Kabal, but that's about it). Kung Lao used to be a solid utility character as well, but I haven't had enough time with the new patch to discern just how well he holds up now.
Of course, it really depends on who you're comfortable with as well. If Raiden and Kabal don't click for you, don't expect them to save you from your bad matchups. Sektor is also a great utility character, from my experience, because he seems to have so few bad matchups; he's a very well-rounded character, with strong defense/zoning and solid offense as well. Cyrax isn't a bad secondary either, he seems to be mostly 5-5 and 6-4 across the board. He has bad matchups, but he should still cover most of yours.
I main sub and my alt characters are Noob and Ermac. I dont know if they compliment subby well but thats just who I use lol.
Well, most of Sub's worst matchups are the ones where he gets hopelessly outzoned. Noob has a much easier time with those, so he's not a bad secondary for Sub. Both characters still get absolutely raped by Kabal right now, but incidentally, Ermac has an okay time in that matchup; his force push makes Kabal's zoning a little more manageable, and his D1 beats the run cancel block string. Truth be told, Ermac and Noob sould cover most of your bad matchups. Some people think Kung Lao stomps all three characters, but I really don't think the matchup is THAT bad for Sub, no worse than 6-4 Lao.
My top four, for a long time, was Cyber Sub > Sub > Noob > Ermac. That worked out for me pretty well. Right now, I'd say it's more like Cyber Sub > Sub > Noob > Sektor > Ermac, possibly Cyrax in place of Ermac.
