As a random thing, I remember my friend telling me that people felt Ayane-Pai matchup was 6-4 in Ayane's favor. I'd have to disagree with that one.
Pai can beat out most every one of Ayane's mix-ups after her 66KK4 lock, and Pai's 66H+K is amazing against defensive rolling Ayane's, mostly because of the distance traveled and the fairly powerful combo she can get off of it (assuming they hit her BT). And, of course, Pai's mid-kick holds give her a nice chunk of guaranteed damage, and her mid-punch holds leave her in a really great position to go for a CB combo or throw loop. Since most of Ayane's moves revolve around those two, and the fact that Pai can easily break Ayane out of her stance dancing as well as ignore some of her frame traps, I think that match-up is more 5-5 or 4-6 in Pai's favor.
Your general overview is a bit inaccurate, because of what I highlighted. For one, rolling and 66KK4 does not make or break Ayane. Ayane shouldn't even be rolling all that much, as it is an obvious cry for getting counter hit too easily. Rolling is not for defense either, it is another option within' her integrated movement. Which is supposed to be used for baiting button presses, catching standstill opponents with slow reactions, and punishing badly placed pokes or moves from a distance (this is assuming BT 6H+P is used).
Furthermore, every character has access to the mid punch hold and the mid kick hold. And while some do more than others, I'll agree that Pai's holds do give her some nice damage when she holds either option. However, that fact does not scare Ayane from using her range tools and keep away tools. And you also cannot overlook the range of her BT2P and BT2K lows either, especially BT2K. I don't think you realize how much range some of her range pokes actually have (take a look at her BT4H+K).
Ayane does a very good job of keeping Pai at a distance and making her pay harshly if she makes a mistake. One of the biggest things Ayane does really well is baiting out responses from her opponents. With 66KK4, their jabs will tie, not a big deal. Don't ignore the fact that Ayane can do BT8P after 66KK4 either, which is a great option because almost every player feels the need to challenge the +1 after a blocked 66KK4. Ayane also has a higher damage output, although Pai's damage is nothing to laugh at either.
Ayane can deal with 9/11/12 just fine, just doing a simple P > BT8P already puts her in a good position because she gets away from you for free and initially set you up for button presses for her to punish. And no, Pai does not punish Ayane's "stance dancing".
I don't know who you've been playing, but they're not making good use of Ayane's tools if they are relying on 66KK4 and rolling often. And I'm quite sure they are using 66KK4 as a range poke, lol.