>>27623348M-Heracross is exclusive to Y and M-Pinsir is exclusive to X. They were also version exclusives in Gen 5. And in Gen 3 they were Mach/Acro bike area exclusives in the safari zone while Scyther was nowhere to be found.
Gen 2 and 4 are just exceptions because Gen 2 introduced it and that would be stupid to make a new Pokemon exclusive to one game when the old Pokemon is exclusive to the other, and Gen 4 has the remake of that. So in 3/5 cases, they're counterparts. That wasn't even true for all of Gen 4. Platinum had Scyther and Pinsir completely unrelated(but Heracross was still stuck in the honey tree meme reference to Gen 2's headbutting trees)
Scyther and Pinsir weren't even counterparts in Gen 2. They were just both high tier bugs for the bug catching competition, as much of a counterpart as Pinsir is with Venonat.