For both greninja and megaman, two characters who have severe roadblock issues with shiek, i have a remarkably similar feeling. Every time I am doing anything in neutral, I'm thinking about how I shouldn't be able to get away with what im doing. Shiek just dominates such an area around her with her burst mobility, she outbuttons you because of fairs insane range, once she wins neutral with fair she can follow up supremely well since a grab leads to kills. If you sit back to figure out how to deal with fair, needles just eat you alive/beat all your projectiles, buttons... why, why why why are needles, little pieces of metal, transcendent, a property of lasers.
Worth mentioning is things have gotten better for ninja since the shield stun buff. Before that, his issue was everything he did she just popped out of shield and fair planed you. I know this is a huge callback and we basically forget the times before this major change, but im so glad they did it. It was a genius decision, basically turning safety from a property of shiek to a usable tool for most of the cast. This is relevant now because greninja's bad startup from nair/fair ,and shiek's extremely low profile from a crouch means good shieks will get a lot of powershields.
I haven't played greninja in a long time so I won't say much about the shiek MU (since she has so much progress on her meta, im sure the MU has changed), but I do have megaman input. The ways i've found to deal with shiek is to be obnoxiously, ridiculously safe as soon as u-air starts killing. Rage is your best friend, and you can win the MU even if she deals twice the damage. I also think a proactive neutral is important, if you slow everything down then you will just lose to fair and needles. You need some hectic action so a stray metal blade will confirm a utilt, she'll make a bad nair on shield near the ledge, or try and challenge bair... just, something that gives her an early death and you surviving forever, and her winning neutral 75% of the time won't matter. This is doable on battlefield, and basically impossible when she can confirm a d-throw uair kill on small stages.
Also, greninjas, you know how people shouldn't airdodge your 5050s unless they want a horrific death? No one should ever die to vanish 50/50 unless the uair will kill you too, airdodging and dying to vanish when uair wont kill you is ridiculously greedy.