Ok. Let's make a list of possible things that prevent a Pokemon to be sent into a IV generation game of the franchise:
-Knows HM
-You have already done the Pokemon transfer at least once within 24 hours.
-"Special adjustments" (i.e. hacked Pokemon, hacked stats, even hacked ribbons of achievement)
-"Special Edition" (This has happened to a friend of mine. It was a shiny, Japanese Sceptile that he supposedly earned for wining a battle competition. It turned that it was a hacked tournament, and it gave a Pokemon that wouldn't allow him to activate the Pokemon Transfer to only that Pokemon)
Send me a Visitor Message and I'll try to help you out even further.