She doesn't only work with substitution, she uses it as a base for being sneaky.
She's fresh from the academy, what other stealth techniques could she have learned without a clan? Realistically, none. Yet her sensei wanted to see more. It's the job of a jonin sensei to expand their genin's repertoire, not the academy instructors'.
To be fair, jonin in this quest are a BIG DEAL.
They only take the best of the best, the most promising, in their teams (and only if they feel like it!), and every single one of their students is guaranteed to reach at least special jounin level, if not outright jonin (unless they die of course).
They're the elite of the village, the top 1% (if not top 0.1%)
Also the team they take becomes pretty much a second family to them, and while they're teaching they can't take any B to S rank missions.
Yui was both unlucky (She had REN in her team!) and, yes, a bit too focused on her one jutsu.
And so she lost her (first) chance to a big name sensei.
She's still a ninja though! Worst case scenario, she'll have to climb through the genin corps while trying to get a special jounin's or an experienced chunin's attention.
She's still friends with some very talented genin and can probably get a few tips and lessons from our teachers if we ask nicely once they get to know, trust and like us.
And if she can impress Asuma, Kurenai or whoever is team 8's sensei, they can certainly put a good word for her.
Short version: she was unlucky, but she has options! This is just a small setback