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what is the purpose of high/low//mid/overhead mix ups?

The point of a mix up is to break through your opponents defenses to land damage. Yes, that means blocking. Mixups can also be used to bait out attacks and then punish. Like after a knockdown, you do the same followup 3 times. After the next knockdown, your opponent thinks your going to repeat the same pattern but instead you do something different thus a mix up. And maybe landing damage.

You can't defend against everything with one method. For instance in this MK, you can't break throws crouching. Vs an opponent who has a threatening low attack, crouch blocking comes natural. If they mix this in with throws, the opponent can't hold on to crouch block out of fear of the throw. Characters with powerful mixups can be hard to defend against because their mixups can keep you guessing.
 
Okay I understand the concept here. Applying it is a feat in itself!

I see all these 11 hit combos and have successfully pulled off the reptile elbow dash one but I find it nearly impossible to land vs hard/expert ai since they block everything. I find against good blocking ai (and future players I would imagine) doing simple 1,2,2 and 1,2,b+2 or 1,2,slide/1,2,dash better since I can hit the string that will break through the standing or ducking defense.

The big ass youtube 11+ hit combos always start 3,2,1 and thus can't hit crouch blocking making the entire combo rather useless.

As for putting this all into effect, how can I do this if I myself am blocking? I find myself most of the time block-stunned and can't land a hit as I am 1,1,1 spammed by scorpions and the like.