B3 should always be used by itself, with B4 followup, or with EN roll followup for mixups. If they block B3, they'll be in crouch. So a ground sai can be beaten out by an uppercut.
I'm starting to think Mileena does give Cyrax problems. What does he have tool wise to counter her? Seems like as long as she doesn't trade with a net she's always at the advantage due to keepout.
Her mixup off of blocked jump in punch is pretty great actually. She has U4, B3~roll, B3, B4 and B3~EN roll. Or she can just throw or use a canned string for block pressure. She can also use these mixups after telekick on hit, as well as F3 on hit. Fuzzy guarding her is harder than most think.