EU faces several challenges, predominately due to significant differences in history, culture, and consequently political and economic traditions. More recently, in addition to misunderstanding with Greece and Britain, EU has been also struggling with regards to the assimilation of Central and Eastern European countries. One of the main reasons for this is that:

Most of these countries had, till recently, command economy and thus have difficulties assimilating

Most of these countries went through political revolutions leading to significant instabilities

Most of these countries are developed economies with significantly different cultural values

Most of these countries voted against further growth of EU and have threatened to exist