first thing that i look at is if they have a way around clone, and if that way is meterless or if it requires resources. ww, for example, has a multiple ways to hit sub through clone that don't require meter, whereas green lantern can shoot through it but he has to spend a bar. often that's not worth it for gl. scarecrow has normals to reach through it, but if you space yourself right they are often not real options for him, whereas catwoman can use db3 or j2 with less risk. brainiac i see as a big issue for this reason as well. there is a giant difference between a so-so brainiac and a really good one, maybe the biggest skill gap in the game imo. good ones will always neutralize clone with his high trait shot, which means you won't be able to rely on cloning defensively when he approaches from the air. he's not great when cornered, but no one is great when cornered vs sub and a good brainiac isn't easy to force anywhere.
back to clone, many characters don't have a way around clone at all, and the fact that sub can hide behind clone is huge. this means anyone with a ftd move (aquaman) is a factor. obviously that doesn't mean ftd moves = bad matchup, but it neutralizes a part of the mind game mid screen when clone comes into play.
the next thing i look at is how slide will affect a matchup. in some cases, like w/ fate, slide and mb ice ball are huge because his projectile options are actually somewhat limited (good mu for sub), whereas vs arrow or a good deadshot (who is utilizing trick shot instead of wrist cannon/low shot spam), slide is not as impactful. arrow is hard to me. deadshot i see as either 5-5 or a debatable 4-6 for sub. slide is also less affective vs superman, which is a mu i personally dislike although i'm not convinced it's bad for sub.
one thing i see a lot of people saying that "so-and-so is bad in the corner, so it's a good mu for sub". corner talk is no longer relevant as far as i'm concerned, because imo sub's corner game is so strong that if you're doing it right you shouldn't be eating wakeups, no matter how good the wakeup is. who the opponent plays is just not that big of a deal because it's all the same- they can either do risky things to try to get out which will likely not work, or they can block and eat throws or w/e you want to do.
sub is consistently underestimated for some reason, but i have always maintained that the tools he has are by themselves very strong. there's no equivalent in this game to sub's slide (gap closer, wakeup, and offensive move that hits low and knocks into clone), just like there's no equivalent to mb ice ball (clears all projectiles on screen and freezes on hit to punish bad zoning), and of course the clone. if he was unplayably bad mid screen then he would be low tier, but he's not unplayably bad mid screen and in the corner, well you get the point.