Anatolia still had a large Greek population in 1900, though it had been dwindling ever since the original ottoman conquest, but many were killed in the Greek genocide, and the rest were deported to Greece in 1923. Roman national identity in Anatolia had also been dwindling for a few centuries, being replaced by an exclusively greek one, though there were likely people left who held on to their identities, as there had been on the island of Lemnos before the greek occupation.

Potentially it could be the religious difference. The majority of anatolia (apart from Trezibond I think) had been controlled by Turkic Muslim beyliks for centuries before they were united again by the Ottoman Empire. Conversely the only Muslim ruler in the Balkans were the Ottomans who in general took a very passive approach to religion, prefering the jizya to conversion. I doubt the Ottomans themselves did much of the assimilation of the anatolian byzantines, but relied on the work of their less tolerant Turkic forebears.