Turkey is headed in the wrong direction at the moment, but hardly to the extent that would endanger its status as a leading light for Muslim nations - politically, religiously, economically. Indonesia - lest anyone forget, the biggest Muslim nation by far - is doing quite well, though we wouldn't want Jokowi to become the Asian Obama.
There are, admittedly, few countries in the world for whom Pakistan might be considered a beacon or positive example. Quite a few of those are Arab countries, though. Unlike any Arab country besides Lebanon and Tunisia, Pakistan recently saw a democratically elected government take over peacefully from another democratically elected government, with still other parties being also influential - their freedom isn't actually that bad. Does that compensate for all the violence and dysfunctionality - probably not, but looking ahead to the future, it might have a brighter future than, say, Egypt. Iran has different strong points, and a future that is really rather undecided, but if it moves the right way, a lot of potential.
Look at a Freedom House map - Indonesia, Pakistan, Turkey, Nigeria and Bangladesh are "partly free" while India is considered fully free (in the most recent version). Those countries between them constitute well over half of the world's Muslim population. But among Arab countries, only Libya, Tunisia, Morocco, Lebanon and Kuwait rank as "partly free" - all small countries except Morocco. FH also added Pakistan to its list of "electoral democracies", with the same argument I used.
The thing is, with the partial exception of Iran and Turkey, in most of these countries, for the majority of their people, a theological reform of Islam as a religion wouldn't make all that much difference. Many of them are Sufis, many identify as Muslim while being ignorant of basic tenets in a way that would (and does) horrify religious Arabs - largely, of course, because Islam always insisted on being at heart a monolingual religion, and non-Arabs who don't speak Arabic aren't taken very seriously. Islam is a rallying point for them, a marker of group identity, and a guarantor of traditional customs - whether or not said customs have anything to do with the original Islam. This goes for Indonesia as well as for Albania, Nigeria as well as Kazakhstan. It's local progress in their local societies that they need. Of course that goes to some extent also for the Arab countries - Tunisia proved quite conclusively that local factors have a stronger effect on the outcome of a political conflict than any region-wide phenomenon.
That said, obviously there are proselytizing and radicalizing individuals and groups that try not only to influence their own neighbours, but also to infiltate in Muslim countries with quite different local traditions (or Muslim neighbourhoods in Western countries), and those have to be fought. But in order to do that, it's absolutely imperative that you rob them of their strongest weapon - their eternal argument of "let us join together as Muslim brothers, despite our differences, and defend our religion Islam which is under attack globally". If they can't use that argument, if they have to make their revolting case purely on its own merits, they'd be rather less successful.
And that certainly requires words and actions from the silent majority in Muslim countries, but also from us in the West. There is nothing wrong with being Muslim; there is no incompatibility between democracy and Islam; and "Islam" is not under attack.