The nucleation and growth of zinc-phthalocyanine (ZnPc) thin films on Ag(100) surface are studied employing in situ, real-time low-energy electron microscopy (LEEM) and complementary DFT calculation to elucidate the role of incorporation kinetics of planar molecules in phase selection during nucleation, and apply this knowledge to fabrication of highly crystalline ZnPc films. We show that the nucleation of crystalline ZnPc islands requires a large concentration of diffusing molecules. The required amount of nominal deposition to initiate growth of ML high 2D crystalline islands is dependent on both, growth temperature and crystalline phase. At room temperature and slightly above (RT to ~430 K), ZnPc crystalline islands have double-domain R33.69 structure, with average domain size in sub-micrometer range. At higher temperatures, a 5x5 commensurate ZnPc structure nucleates. DFT calculations reveal significant differences in interfacial energies of an isolated ZnPc molecule on substrate, depending on an adsorption site and azimuthal orientation of the molecule relative to the substrate atomic lattice. The observed delay in the onset of the nucleation of an island is caused by existence of a large energy barrier for molecule incorporation into an island. At certain growth conditions it is possible to induce a structural transition from 5x5 to R33.69 phase, when the nominal coverage reaches 1ML. The resulting film has excellent crystallinity, with individual domains of hundreds of micrometers in size.