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One big reason: educational games have fallen out of favour within school systems. Many teachers were simply using them as incentives, rather than using them as guided educational tools. Without the guidance, these games had minimal value for learning. Of course, the value of the educational content also varied a lot. Even the good ones depended a lot on rote memorization, which cyclically goes into and out of favour among educators.

In this case, the other issue is that Minecraft is pure entertainment software. It may have educational value, but the origin of the game makes it a hard sell. (Civilization and SimCity faced similar problems.)