Modern Learning Environments without the Pedagogy- Building a Plane In the Air?

Well, MLE's are the flavour of the year, aren't they?  I want to get on my high horse over this one.  I have seen MLE's fail in a number of schools.  It is not that the idea behind it is not an excellent one. It is just that those schools have not looked at the reasons for change closely, nor have they looked at the pedagogy behind the concept and so teachers have been caught unawares, ill-prepared and doomed to failure.  It has left a bad taste in the mouths of the schools and their communities, who saw their students start to "run wild" without structure to their schedules.  It has put those schools back to square one with a lot of rebuilding and public relations to be done.
The schools went into the MLE with good intentions but eyes shut.  These changes take a lot of planning.  Time for all involved to settle down to establish a clear vision, set strategic intentions and goals, provide targeted professional development for teachers, engage in consultation and dialogue with the community, establish agreed outcomes, develop a long term plan and a short term plan.  Years not months.
I started writing about this a few weeks back but got inspired to say more when this blog by Karyn at Te Karaka School caught my eye in my facebook feed (via Rebbecca Sweeney).   Karyn asks teachers and schools to lots of questions about what they are doing and how they are doing it.
I started thinking again about the tension between striving to meet school goals around numeracy and literacy, or NCEA and the seemingly opposing pull toward future focused personalised learning, nurturing of individual talents and abilities, and desiloing of schools, with establishment of contextual learning in the "real world."
It seems to me that the short term numeracy, literacy and NCEA goals are looming too large in the teachers' worlds.  I am not a primary school teacher but a secondary one.  NCEA can and does open up opportunities for a lot more peronalised learning pathways, but not within the existing timetable  restrictions that many schools place on themsleves because that is the way they have always done it.
How do we build this plane while it is flying?