Motivated by a goal of realizing spin-orbit coupling (SOC) beyond one-dimension (1D), we propose and analyze a method to generate an effective 2D SOC in bilayer BECs with laser-assisted interlayer tunneling. We show that an interplay between the inter-layer tunneling, SOC and intra-layer atomic interaction can give rise to diverse ground state configurations. In particular, the system undergoes a transition to a new type of stripe phase which spontaneously breaks the time-reversal symmetry. Different from the ordinary Rashba-type SOC, a fractionalized skyrmion lattice emerges spontaneously in the bilayer system without external traps. Furthermore, we predict the occurrence of a tetracritical point in the phase diagram of the bilayer BECs, where four different phases merge together. The origin of the emerging different phases is elucidated.