Production of electron bunches with extremely small transverse emittance is the focus of the PITZ (Photo Injector Test facility at DESY in Zeuthen) scientific program. PITZ is one of the leading laboratories on generation and optimization of high brightness electron bunches with different charges for free electron laser (FEL) machines such as FLASH and the European XFEL. In 2011 using a photocathode laser with a flattop temporal profile, PITZ has revealed record low transverse properties emittance values at different bunch charges. However, further improvement of beam quality with smaller emittance is foreseen using a cathode laser system, capable of producing 3D ellipsoidal bunches. Numerical simulations were performed to study and compare the beam dynamics of electron beams produced with 3D ellipsoidal and flattop laser profiles. Different bunch charges from 20 pC up to 4 nC are considered in the simulation, in order to find an optimum PITZ machine setup which yields the lowest transverse emittance. In the present paper, the simulation setup, conditions, and results of the comparison are presented and discussed.