The blame is cast in many directions – to parents for pressuring elementary schools out of fear that their children won't get into the right high school, to high schools for placing a premium on gemara education, to school administrations and teachers for poor time management. I don't know enough to comment.
Here's an interesting take, though, on the central cause: According to Maharsha, writing in 16th century Poland, the problem is one of arrogance.
The Talmud (Sanhedrin 24a) links the name בבל (Babylon) with the word בלולה (mixed-up), to say that in Bavel their learning is a mixture of Tanach, mishnah and talmud (meaning analytic study).
The gemara there does not state whether this is a positive or negative, and Tosafot there actually sounds like it is a feature rather than a design flaw, but Rabbi Yirmiyah adds what certainly sounds like criticism: "Eichah 3 says, 'Gd placed me in darkness, like the dead of eternity' – This is the study of Bavel."
Maharsha there explains:
"As a result of their arrogance, their learning is all mixed up and out of order; the one who should learn Tanach at 5 is studying mishnah, the one who should be learning mishnah at 10 is learning talmud. In their youth they learn a mix of mishnah and talmud, as a result of their arrogance.
"Rabbi Yirmiyah said regarding this, 'They placed me in darkness' – The prophet Yirmiyah (not to be confused with Rabbi Yirmiyah) declared this regarding the Babylonian exile, and Rabbi Yirmiyah used it regarding himself, for he was Babylonian and he had learned in that mixed-up system."
So the gemara's line is not describing the multidisciplinary nature of Babylonian Talmud. Rather, it's criticizing the educational approach in Babylonian schools, teaching children Mishnah and Talmud before they are ready.
What does the Maharsha mean? What's the connection between arrogance and starting kids on gemara too early?
Is he saying that parents pressure teachers and schools because they want to believe their children are precocious?
Or does he mean that teachers and administration rush students into the advanced curriculum to build/maintain a school's reputation?
I'm not anything resembling an expert, but I wonder what the Maharsha meant.
אמר רבי יוחנן בלולה במקרא בלולה במשנה בלולה בתלמוד +איכה ג'+ במחשכים הושיבני כמתי עולם אמר רבי ירמיה זה תלמודה של בבלMaharsha's text:
והוא שמתוך גאותן לומדין בלול ומעורבב לפי הזמן דבן ה' למקרא לומדין משנה ובן י' למשנה לומדין תלמוד שבקטנותן לומדין מעורבב משנה ותלמוד מתוך גאותן וקאמר רבי ירמיה על זה במחשכים הושיבני וגו' ירמיה הנביא אמר האי קרא על גלות בבל ואמרו רבי ירמיה גם כן לסימן על עצמו שהיה מבבל ולמד שם תלמודם מבולבל ומעורב