A lot of players, good and bad, feel that Sub-Zero absolutely owns this match. How many times do you pick Reptile, only to see your opponent quickly run to Sub-Zero as a counterpick? I love when that happens! Sub-Zero is the easiest match for me to win with Reptile, personally.
REPTILE
Invisibility + keep your distance = you control the match. From this position, Sub-Zero can only do a few things, and you can counter them all. You can duck under his freezes and instant acid spit (you won't ever get frozen if timed right). You can anticipate slides, block and punish. Or you can anti-air when Subby jumps in. Ninjas are all weak when it comes to CQC, but that's what makes it so much fun to play in close with them against each other. Especially if you're invisible, you can really toy with Sub-Zero up close. Forceball takes so long to get out, that it is risky against Sub-Zero. But throw some in when Subz is jumping away, or at other times when it appears he won't have time to freeze you. Slide gets under the freeze sometimes, but other times it doesn't. You don't want to be eating jump kick/ground freeze combos from Sub-Zero, so use caution with your slides.
SUB-ZERO
You definitely want to make this a match of traded projectiles. Getting hit by an acid spit, but in return freezing Reptile and scoring a jump kick/ground freeze/uppercut combo is a good trade-off. Up close Sub-Zero has the better CQC by means of his ground freeze. It is tempting to turtle with Sub-Zero in any match. But if Reptile goes invisible, it can spell real trouble for Subz. Try to be aggressive enough that he never goes invisible. Anti-air any jump ins with roundhouse of course. Also be prepared to block Reptile's slides and punish them.
Reptile has more options in this one. You know what you're gonna get from Sub-Zero, but Reptile can be hard to predict. Also Sub-Zero's projectiles do no chip damage if blocked, whereas Reptile's do. Still, Sub-Zero's freeze combos are massive compared to Reptiles, so he has a slight edge.
6-4 for Sub-Zero.