The reason I find it an annoying matchup (not bad, but annoying), is because clone blows up your pressure as a better option than what about every other character has. For example, after fly kick MB, subzero can EX clone and suddenly be ahead in neutral. It covers every liu kang option. Similarily, cancels like F44 that don't actually jail people normally have to respect, but subzero gets a free clone during that moment so that if LK tries to read armor, he gets frozen, if he tries to pressure, he gets froze. It covers several liu kang options with a single input, thats the value.
The other thing is I find it very hard as LK to deal with his Subzero when you are in the corner. When Liu Kang is knocked down and SZ sets up a clone, all Liu has as wakeups are highs. Meaning Sub can just D1 outside the range so that only if you armor will it hit. That makes all your wakeups miss by either flying over him, or get hit by a D1. A lot of characters can combat Subzero corner pressure using Neutral Jumps, but Liu Kang's is god awful, so that option is basically removed.
As Liu Kang, you need to make more reads on the Subzero player, than he has to make on you. Thats why this matchup is annoying... With that said, its nothing worse than a 4-6, and I think I'd still consider it a 5-5. I'm not xarakamaka though, so what I say doesn't hold much ground.