"But going from surprise attacks into combo, into fatal blow is just a joke looking at it."
I think it's fine and you pretty much answered it here by yourself. 50%+ damage can only come from either a very unsafe move or a krushing blow or if you are cornered. Basically, it depends on you. The solution is, don't get hit by it. And be even more careful when opponent is under 30%.
Damage form fatal blows scales a lot though. It's usually over 300 but when you are already in a combo of 200+ damage, fatal blow might be halved or more reduced.
Since you are using Scorpion as an example, his F34 is a krushing blow if it's a punish or a kounter. If you follow with amplified teleport, F32, amplified spear, F32 again, you do 363 damage. Usually you'd end that with DF4 but if you end it with fatal blow, you end up with 476 damage. So your fatal blow did only 114 damage instead of 310.
Now F34 which started this is not unsafe but it has 13 frame start up. So you either did a very unsafe move or your attacked whipped which resulted in a kounter and krushing blow which means you lost footsie game.
But you are also forgetting that so damaging kombos are usually juggles which can be escaped by breakaway. So yeah, I think it's fair.
