While I will leave the details to someone better suited I can refer you to an explanation given by J. R. Hamilton in the introduction of Selincourts translation of Arian the campaigns of Alexander.

While the exact belief and intentions of Alexander can never be known it is recorded that in his prayer at Opis he wished that "Macedonians and Persians might live in harmony and jointly rule the empire". In other words Alexanders wished the Macedonians to see their now conquered opponents as their equals.

This flied in the face of everything the soldiers grew up on that the Persians were uncultured barbarians who posed a threat to their freedom and who they where fighting to avenge the atrocity's committed against them in the previous war.

Hamilton writes that Alexanders teacher Aristotle is said by Plutarch to have "written to Alexander advising the young king to behave towards the Greeks as a leader but towards the "barbarians" as a master". This gives insight into the feelings of the time that the Persians were not their equals or comrade in arms but conquered foes who should be treated as lesser beings.

To add to all this is a second insult in that Alexanders soldiers who had fought by Alexanders side from battle to battle and siege to siege felt they were being unceremoniously replaced by the next generation (by barbarians no less) who didn't suffer with them against all the odds but where instead becoming the soldiers who would reap in the glory that they had fought for. i.e the old guard can tend to resent the new guard at even the best of times.

In conclusion Alexander had already taken on Persian manners and dress so, while he might have wished to train the Persian boys in the Macedonian style of fighting to show his loyalty to His homeland, it was still seen as an in bulk replacing of the soldiers who had won him his empire by his new beloved young Persians.

To further /u/Kindestchains comment, there was considerable disdain for easteners or Asiatics by the Greeks. Philosophers like Hippocrates felt that Asiatics were slavish by nature due to their easier standard of living (Mesopotamia had much nicer soil than rocky Greece) and this would be compounded by their monarchy which only reinforced this slavish nature.

The Greeks on the other hand (he wrote in mid 5th to early 4th BCE) were brought up in a tougher clime and their system of government made them better.

So these attitudes about any non-Greeks were pretty ingrained. Plus the pikemen in the army were called pezetairos or "companions" to the king. That meant quite a bit to them and the addition of these 'slave-by-nature' Asiatics would have diluted that sense of elilteness.