One factor to keep in mind regarding the annexation of Kosovo is the religious issue. Though, from a western point of view, Albania is one of the most ethnically homogeneous nations in the Balkans (due to it's small size), religiously it is quite heterogeneous. With a religious breakdown of roughly 70% Muslim (20% of those belonging to a liberal sect known as the Bektashi), 20% Orthodox, and 10% Catholic religion has the potential to become a bit of an issue. And indeed as evidenced by Greek Orthodox involvement in the near Civil war of the mid 1990's it has in OTL.
Now Kosovo's religious breakdown is more simple. The vast majority of Albanian Kosovars are Sunni Muslim with only a very small number of Catholics. Thus the annexation of Kosovo would fundamentally alter the religious composition of Albania giving the Sunni Muslims a sizeable majority and therefore the potential to threaten the rights and lives of the other religious minority communities (at least in their own minds). If you add in the Serbian community, this makes things even more complicated.
HOWEVER: I think one of the best, most overlooked POD's for a "Greater Albania" is found in the late 1940's with the ascension of Enver Hoxha. It's common knowledge that immediately after WWII Albania and Yugoslavia were quite close, so close that plans had been all but finalized to incorporate Albania into Yugoslavia as the 6th Republic. The Albanian Republic was to be given Kosovo, a slice of Southern Montenegro, and the Western Counties of Macedonia in addition to a great deal of local autonomy. This plan was ultimately derailed by the ascension of Enver Hoxha who overthrew the pro-Yugoslav wing of the Albanian communist party and instead pursued a policy of fear mongering and isolationism, generously described as "bat-shit crazy" for the next 40 years or so.