You're right, Yagura was under control for years and he was a perfect jinchuuriki. High chakra pool and control won't help you against a high level sharingan genjutsu
Exactly. The only known ways to get out of a Genjutsu are:
1. Realizing the weakness of the Genjutsu making it far easier to break. Which is why the Sharingan helps against the Genjutsu; because it can detect said weakness in the illusion.
2. Disrupting the chakra of the one affected. This is why characters such as Naruto and Bee are immune to Genjutsu, because they always have someone who can disrupt their chakra (aka the tailed beasts).
The hundred seal doesn't give any of those advantages to Sukura and thus, it's borderline useless against Genjutsu's.