So the controversy was over a previous draft of the speech:

Among the activities the government initially suggested for prekindergarten to sixth-grade students: that they “write letters to themselves about what they can do to help the president.”

The speech was rewritten. Controversy over.

It is worth noting however that much of the reporting on this omits the controversial part of the speech, instead choosing to frame it this way:

The uproar over the speech, in which Mr. Obama intends to urge students to work hard and stay in school…