As a Ninjutsu specialist, even I don't believe that Scorpion's EX Teleport needs armor outside of wake-up. That would be a little crazy for my tastes.
Now a faster start-up for EX Takedown? I'd take that.
Don't forget, though, you have an impressive arsenal of crouch normals to challenge their offense with. Your D1 is 6 frames, D3 is 7 and D4 is 8, and all are useful in their own way including interrupting staggers.
I'd also experiment with cancelling your pokes into a fake teleport regardless of whether they hit or are blocked so as to get yourself out of dodge.
EDIT: His 7-frame S3 deserves an honorable mention for when it comes to challenging staggers. It's effective against Kotal Kahn, as an example, way more so than S1.