User blog comment:Saratje/Hermaeus Mora's true plan - control the dragons? (minor spoilers)/@comment-13446185-20140117042949

Alduin is a literal god, an equivalent to Shor, no being would be able to control his mind.

Plus Mora is a rather content deity, he doesn't need anything other than his knowledge, doing something as ambitious as mind controlling all dragons isn't really in character for him. The more obvious answer in my opinion would be that Mora purposefully let Miraak escape Apocrypha in order to pressure the Skaal into giving up their forbidden knowledge to him (Anything an omniscient being does not know must be unbelievably important).