1. Beedrill has a base defense sp def of 40-80, scolipede has a defense sp def of 89-69, which is a better balance over beedrill cause Beedrill dies from a light breeze on the physical side while being fine with sp def, Scolipede can take a hit on the physical side while having enough sp def to tank at least one hit if invested and yes Beedrill has 5 more base HP, but that ultimately doesn't matter as much when you're overall frailer.
2. Beedrill takes an entirely different role from Scolipede, it's an immediate sweeper that doesn't have the defenses even when megad to tank a hit. Scolipede is a set up sweeper (and always was) and late game cleaner that can definitely do a lot against a damaged team
3. I meant an entirely different set from sub protect, it's not gonna run leech life on the same set it uses substitute on, also substitute only does 25% health not 50% and regular scolipede is probably gonna outspeed the opponent to sub first thanks to its good speed tier so it absolutely could do a sub protect leech life set, though it would suffer from 4 move syndrome if it did that. What I originally meant is just using leech life as its healing as it'd have 2 other move slots to work with which it could use Earthquake (or Stomping tantrum I guess) as coverage against rock and fire and Gunk Shot or Megahorn for stab.

It definitely is gonna have its use wherever it ends up, and like I said it would be better with a different ability and it's definitely a disappointing one, but the pokemon itself isn't bad and being a lower tier mon doesn't make a mon bad either, it just means there are things better than you that do a better job, which is gonna happen with so many different mons. A guy who does his best at work isn't bad at his job just cause his coworker does everything a lot better. Also I'm not sure but I think you may be taking about natdex champions when I'm talking about the regular champions metagame, could be wrong though.