It is not so much that Islam was not accepted or that people didn't convert, but rather that most traces of it were later removed. Starting with Bosnia for a comparison, it is not fully Islamic. Out of three major religions in Bosnia (Islam, Catholic and Orthodox Christianity) Islam is relatively most numerous however still under 50% in absolute numbers.

Islam was not insignificant in Greece or Croatia. For Greece I can only say something about Thessaloniki (and that based on an excellent Salonica: City of Ghosts by Mazower), where Islam was also one of three major religions (Orthodox Christianity, Judaism and Islam in this case) until Muslims - Turks (one being identified with other in practice) were expelled early in 20th century, starting with Balkan wars and ending with Greek - Turkish population exchanges.

In Croatia, very similar thing happened but a bit further back. Slavonia, part of Croatia, was a part of Ottoman empire for some two centuries, as were large parts of Hungary. However, after Hapsburgs (re)conquered those parts (concluding with a peace in 1699 and 1718), Muslims were presented with a choice of converting or expulsion, all mosques were destroyed alongside with most architectural or monumental signs of Islamic presence. Today you would be hard pressed to find a mosque or a long standing Muslim community in Slavonia. It makes it very easy to forget those Ottoman centuries, and multi-religious coexistence.

By the time Hapsburgs occupied (in 1878) and annexed (in 1908) Bosnia and Hercegovina, such policies were no longer considered practical, even though Greek example from early 20th century shows that they were not unthinkable. If nothing else, it would be a great destabilization of the region and depopulation of Bosnia. So, to conclude, the question is not why other areas didn't embrace Islam, they largely did, but how and why Islam remained in Bosnia and Albania.

For one thing, Croatia was never fully under the Ottoman Empire. All the cultural, economic and population centers (coast and Central Croatia) remained free from Ottoman occupation, they were parts of Venice (coast) and Austria/Hungary (Central Croatia).

A more apt comparison to Croatia would be Slovakia or Hungary, countries that spent the same amount of time under Ottomans as Croatia and to roughly the same extent.

Greece is definitely a completely different case than Croatia as Greece was in its entirety part of the Ottoman empire for centuries.