Based on what I've found, I would say that it was a combination of factors that all amplified each other. The conquest of Albania was particularly brutal compared to the rest of the region, and was furthermore contested through the revolt of Gjergj Kastrioti Skënderbeu, which lasted from 1443 through 1468. Even by that time, the region of Krujë had developed into one of the more important subaşilik (an Ottoman gubernatorial region) centers in the Balkans. This basically devestated the area, and led to the emigration of thousands of Albanians to the north (there seems to have been a very large émigré population in Naples because of this)1.
Over the next couple of centuries, the remaining Albanian population was further diluted through the immigration of Muslims from elsewhere in the Ottoman empire. This trend of population movement is noted in many of the contemporary writings and also in traditional accounts of the expansion of Islam into the Balkan regions2.
These demographic trends would have amplified each other as areas with large Muslim populations tended to both serve as magnets for further Muslim resettlement and accelerated the pace at which the rest of the population converted to Islam. This makes quite a bit of sense if you compare it to large regional ethnic concentrations in the United States for example, and I would imagine that similar social dynamics would have been at play. This is actually evident in the tax records for the region, in particular records related to the cizye, or tax on non-believers (thank you Ottomans for keeping good tax records). Population studies based on these records seem to confirm these types of concentrations3.
In addition, this link gives a pretty good summary of the literature and is worth a read.
1 Jelavich, Barbara, History of the Balkans: Eighteen and Nineteenth Centuries, p 34-5
2 Norris, H. T., Islam in the Balkans: Religion and Society Between Europe and the Arab World, p 141-5
3 Minkov, Anton, Conversion to Islam in the Balkans: Kisve Bahas ̧petitions and Ottoman Social Life, 1670-1730, p 43-8