The lack of information and training about beginning reading instruction.
I left teaching in the public and catholic system to immerse myself in learning about effective beginning reading instruction teaching approaches (mortified by the number of students who were struggling along with only band-aid solutions rather than true remediation and therapy). This information is not difficult to find. I now get calls WEEKLY from parents with the same story - their children are doing okay in kindergarten, grade one, and grade two (despite the parents' disbelief), but then are told that their children are struggling as the enter grade three or four. Students with dyslexia or other specific language impairments are not being caught early enough, nor are teachers being trained well enough (using Orton-Gillingham approaches to teaching reading). This is not even touched on in Teacher's College, and when i present workshops to teachers (i have been doing this for 15 years), most teachers are thrilled (no exaggeration) to recieve information about the structure of the english language and basic phonemic awareness (and systematic and explicit phonics) principles and practices.
So good quality training for teachers, along with the bureaucracy of the system (beginning with the Ministry of Education, and flowing down through the literacy consultants in schools) that prevents quality beginning reading instruction training, is the biggest problem preventing schools from being successful.