Humor-wise, SCTV's strength were parody and satire. SNL's was anti-establishment. Even though both shows dug into the same talent pool of Second City, SNL had just as many National Lampoon alums on their staff, which played into the post-Watergate "fuck you" attitude that permeated the country at the time.
To me these two shows (and for SNL I am speaking of the first 5 years) are Astaire and Kelly. They both excel at dance - just in different ways.
I think it's self-evident that SCTV survives the test of time far better than SNL. Yes, both shows were hiring from this talent pool, but the end result could not be more different. SNL was a pressure-cooker, with everyone fighting for their own material to make air (not to mention the drug use), while SCTV had a deliberate pacing that ignored topicality and invested instead in universal memes. Even when they became part of the NBC line-up in the fourth season, they pretty much ignored network notes, and kept doing what they were doing they way they had been doing it for three years. (They were secluded up in Canada, away from network influence, unlike SNL, located at corporate headquarters.)
Just compare them A/B. The complexity of characters is far richer on SCTV: A station owner that rolls around in a wheel-chair purely for sympathy is far more compelling than Goat Boy. Perhaps it's a cheat to use the worst SNL character for comparison, but I can find nothing as thoughtless or knee-jerk in the entire run of SCTV, even on that last season on Cinemax, when they knew it was the end of the road.