I don't think it's really that odd though. Keep in mind that she applied as an in-betweener at Madhouse before getting the gig on Dream Machine. It's important to separate the prestige of the films with the actual work experience.
In the Japanese animation industry, she would be a very new key animator who has never worked at the bottom, and has just 3 years of experience working only on feature films by major directors who specifically selected her to join their team based on her work on a single western film.
Her experience working on The Illusionist probably eclipses all her anime work to date, and as she herself says, it is a very different work environment from how anime is made. So given the context of Anime Mirai, I think it makes a lot of sense that she would be considered a junior key animator and not a senior key animator. Let's not forget that most of the other junior animators at the various studios on Anime Mirai probably have much more experience than she does working on anime, and some have already had the chance to do some animation direction and design work too.
In the end, some animators are just luckier than others, and they meet the right people, or just work on the right projects and become recognized that way. Surely you wouldn't say that she can be put on the same level of experience as the two Madhouse senior key animators on the Anime Mirai project - Hiroyuki Horiuchi and Yuuichi Yakahashi. Could she be a better animator than them in terms of talent? Sure. But that's what training is about - more experienced people leading and guiding less experienced newcomers to be able to polish and showcase their talent better.
Consider Yoshimichi Kameda for a moment. He is in many ways probably one of the luckiest (and most talented) new Japanese animators in the anime industry now. He has only been working in the industry for 5 years now, but instead of being "talent spotted" and working exclusively on feature films, the majority of his work is in fact on TV. This gives him a huge advantage in terms of output, and also in understanding what is expected in normal day-to-day animation production. It also means that his talent was all the more obvious when displayed side by side with his peers, and made under TV deadlines.
For Aya Suzuki, I think that in terms of recognition outside of her work on The Illusionist, it actually worked against her because her anime portfolio as of now would be compared in films next to the very best of the best in the industry. As a foreign animator given a chance to work on scenes in these movies, it is definitely very exciting for her, but at the same time the very best scenes would all be taken up by more prolific and acclaimed animators also working on these projects.
I think when we look at it from that perspective, it makes perfect sense that she would still be considered a junior animator for the purpose of the Anime Mirai project. This is not a negative thing though, and by no means a judgement on the talent or potential of an animator. Instead it could well be a positive thing because it might in fact put the spotlight on her talent, which is what she would need to get more work and higher responsibilities after this.
Meanwhile Kameda doesn't even need any such "training" because when he works on a feature film these days, he is one of the main animation draws along with the other big names, and he is already taking on an Animation Director role on the Layton vs AA project at BONES. So working on TV as opposed to starting out on major films actually worked in his favor instead.
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Wow I didn't expect to write so much, but yeah it was interesting to think about it and put out how I see the different career development paths within the industry work out for different animators we know about.