He's just a random thug in comparison.
Well first of all, I don't see how that's true in either timeline. Objectively speaking, in the new timeline Kano has already done far more, and his feats are far more impressive, than the vast majority of the MK9/MKX roster. Either personally -- he managed to bypass Raiden's wards to steal Shinnok's amulet, and the traps he left behind were strong enough to incapacitate Raiden for a long time. How many characters can boast that kind of power? -- or as leader of the Black Dragon, in which capacity he has bossed Kabal, Tremor, and Erron Black around. If he's just a random thug despite telling them all what to do, what does that make them?
But second, and more importantly...
always liked the idea of it being Sektor who gave him that scar, which also makes more sense, as he's an actual rival to Sub-Zero.
Following this philosophy, any underdeveloped characters would remain underdeveloped, and only those characters who are already developed would continue receiving development. It's nonsense. You have to start somewhere with everyone.
Sektor giving Sub-Zero his scar is pointless because it develops a rivalry that doesn't need any development at this point. We already know that Sektor and Sub-Zero hate one another. They already have a very long history together. The scar adds nothing to that story. Aren't you tired of seeing Sub-Zero fight Sektor? Aren't you tired of seeing Kano fight Sonya? The way to breathe new life into those characters is to use them to tell new stories. And to do that, they have to get pissed at characters they've never been pissed at before.