Because she thought the future of Russia was in Nixa, not the other sons.
If you read about the genesis of primogeniture, its really fascinating. In the beginning, kings would divide their kingdom equally between their sons. That way Charlemagne's son Louis the Pious split up his vast empire between his three sons and Italian noble families split up their inheritance equally between all sons until well into the Renaissance.
However, splitting up property between all one's sons meant that in a few generations after equal splitting of the kingdom between several sons meant that each son's kingdom became smaller and smaller with each generation. After a few generations when the ties of blood became weakened, the cousins would fight bloody battles with each other and the kingdoms became too small to govern effectively.
So it became standard for kings to name one son as the sole heir to the throne. This was the premise of the movie The Lion In Winter, where Henry II of England had to choose his heir among his 3 sons. After awhile even that became less stable as kings on a whim changed who their heir was going to be.
In fact Peter the Great still maintained the right of naming his own heir but by his time, most kings left their kingdoms to the oldest son for the sake of security. People knew who the heir was, he had a lifetime to prepare, and the plan was that there were fewer surprises.
This worked overall surprisingly well, except when the oldest son died. As for why Marie and Alexander stunted the growth and education of their youngest sons I can only think it had to do with the fact that up till a few years previously, the crown of Russia didn't necessarily go to the eldest son. Peter the Great set expectations that his eldest son would not succeed him, Catherine the Great overthrew her husband, Peter the Great was succeeded by his wife Catherine I.
So the tradition of the first son inheriting the throne I don't think was as firmly ensconced in Russia and so Marie and Alexander may have genuinely worried that some of Nixa's brothers would try to overthrow him from the throne and so they sought to blunt their education and make them unimaginative dull creatures so that they would never even think of overthrowing their oldest brother Nixa.
Certainly if Nixa had been alive, the rather unpretentious and methodical Sasha would have never (I believe) led a coup to overthrow his brother. And I think that was the purpose of the difference in education.
However, when Nixa died, it had tragic side effects.
"One thing we can do is make the choice to view the world in a healthy way. We can choose to see the world as safe with only moments of danger rather than seeing the world as dangerous with only moments of safety."
-- Deepak Chopra