You raised an interesting point about classes for like minded, capable, motivated girls who want to learn. I can think of a couple of issues:
1) What we have is Halachic precedent for is girls / women learning Talmud as individuals.There where even (rare) cases of exceptional women who gave shiur (from behind a mechitza) to men. Organized Talmud classes for girls / women is unprecedented. To be sure, that is not insurmountable. After all, Beis Yaacov was also unprecedented. However, like Beis Yaacov, such an innovation should have broad support from Gedolei Yisroel to be considered legitimate.
2) Such initiatives will surely be highjacked by people with a Feminist agenda.
@AAQ
Can you unpack what you mean about “the analysis of Mitzvot”
There are different ways to analyze Mitzvot. Do you mean: (1) legal parameters, like the Talmud. (2) reasons, like the Chinuch. (3) Something else…