Hm... Let's see then, eh?
AP: I'd be betting on Blanka, tbh. Reptile severely downscales from a feat that is exactly twice as much as Blanka's yield, and considering that said downscaling is, indeed, quite significant, at best they'd stand on similar terms, otherwise I'd be inclined to bet on Blanka. In any case, they both have calws and fangs to help even out the AP differences, but they both have some ways of improving their AP: Both have attacks that hit harder and can do enhanced moves that do more damage, Blanka can use electricity, Reptile can use acid. Overall, I say that Blanka has the AP advantage, but both have ways to circumvent that, at least partially.
LS: Reptile has the outright better LS, and not only that, but his smaller frame relative to his greater strength makes it a bit harder for Blanka to grab him. However, while Reptile does have the advantage here in most scenarios, I don't think a victorythrough submission would be viable, because of Blanka's electrical shocks.
Toughness/Stamina: I'd give this to Reptile simply because the average MK fighter goes through much more punishment and serious wounds than the average Street Fighter character. Otherwise, they'd be relatively equal.
Speed/Agility: Oho, now this is interesting. Y'see, from a purely feats standpoint, Reptile is the unquestionable superior here. His surface scaling is nuts, and the way he manages to move in even harsh situations is just astounding. However, in a fight, at least not in cutscenes, Blanka uses and abuses his acrobatics way more than Reptile does, to the point of near inanity, and his straight momentum is far greater than Reptile's. So while the advantage here is probably to Reptile, in practical terms, I wouldn't rule Blanka out.
Skill: This is hard to measure... I mean, I feel tempted to give the edge to Reptile, but that's just because he has more screentime than Blanka and has more statements about his skill than Blanka does. They seem pretty close in general, but Reptile has renown as an assassin and Shao Kahn has commented at least once about Reptile's assassination prowess, treating him with respect. Again, not that much to go by, but it's still a thing. Yet, what little we have seen from Blanka's statements on skill also do seem indicate that he is quite capable, being used to spar to some powerhouses with considerable skill. This is either a tie or a slight advantage to Reptile.
Powers & Abilities: Hmmm... Reptile has a much greater array of abilities, and he does seem to use them well. His adhesive slime and acid in particular are great, and he has way more options than Blanka does to any given situation. His aura can passively damage Blanka and can boost his perception quite significantly. However, Blanka's ES are superior to Reptile's, and Reptile's invisibility, perhaps even stealth should be pretty much negged by him. While Reptile has more options, the ones that Blanka does have make him more dangerous in a straight-up slugfest, such as the crumpling mechanic. He can also have some very interesting methods of moving around with Lightning Mole.
Conclusion: Overall, I'm leaning towards Reptile, with high difficulties. I think that his greater array of powers and LS to keep Blanka at bay will be what'll save the day, and should be enough to grant him a victory over Blanka's superiority in a straight-up slugfest.
