Hydrogen absorption by a thin Mg2Ni film capped with Pd results in the nucleation of the Mg2NiH4 phase at the film/substrate interface. On further hydrogenation, a self-organized two-layer system consisting of a Mg2NiH0.3/Mg2NiH4 bottom-layer and a Mg2NiH0.3 top-layer is formed. This leads to an intermediate optical black state in Mg2Ni thin films, which transforms from metallic/reflective to semiconducting/transparent upon hydrogenation. This hydrogen absorption behavior is completely unexpected, since the hydrogen enters the film through the Pd-capped film surface. To explain the preferential nucleation of Mg2NiH4 at the substrate/film interface, we determine the chemical homogeneity of these thin films by RBS and SIMS. Furthermore by STM, TEM and SEM, we analyze the microstructure. We find that up to a film thickness of 50 nm, the film consists of small grains and clusters of small grains. On further growth, a columnar structure develops. We propose that the nucleation barrier for the formation of the Mg2NiH4 phase is smaller for the small loosely packed grains at the interface, while the columnar grain boundaries promote the hydrogen diffusion to the substrate.