There are at least two potential reasons why it was hard for Sumerian city-states to create empires.  We must, however, note that it is very hard to know for certain why things happened (or did not happen) 5000 years ago.

The first potential reason is cultural or political.  The people of Mesopotamia identified very strongly with their city-states.  Each city state had its own god with whom it was identified.  The people of the city-states felt that they were separate and different from those of other city-states.  This meant that it would be hard for any empire to cause all the city-states to submit willingly to being ruled.

The second potential reason is geographic.  The region of Mesopotamia is not easy to defend from outside attack.  It does not have mountains to protect it.  Its rivers are not hard to cross.  The terrain is relatively easy.  Therefore, it was fairly easy for invading forces to come in from the outside.  These forces could disrupt nascent empires, thus making it difficult for empires to arise and grow large.

These are the two main reasons that we today can discern as to why the Sumerian city-states had a hard time creating empires.