The problem with Motocross engines is that they're all 1 cylinder (except Aprilia) so they would be much less powerful than the current 250cc 2 strokes.
250cc is supposed to be the last step before MotoGP. Currently going from a 120 hp 250cc to 250hp MotoGP is a big step, coming from a 450cc motocross (70 or 80hp) engine, the step would be too big.
Although they idea would be fine for the 125cc category (around 60 hp now).
Something more similar to a MotoGP is needed. Supersport bikes would be a good solution, but they can't be used in World Championship because they are not prototypes and Flamini (World SBK) has got the exclusive rights for road-derived bike racing.
400cc 4 cyl prototipes would have the correct power and weight (around 150hp), they would be a good learning phase for future MotoGP riders. But Aprilia will not want that, they are not in the same 4 stroke tech level as the Japanese companies, so they would veto the proposition.
It's a difficult problem to solve.