I think this problem is similar to the problem of finding modes of rectangular dielectric waveguide. In this case, you can use the effective-index method for finding the approximated solution (For your problem, we can call it effective-potential method). For more information about effective-index method see the following articles:
Effective-index analysis of optical waveguides: Link
Analysis of integrated optical waveguides: variational method and effective-index method with built-in perturbation correction: Link
The basis of this method is that the mode of a waveguide can be separated into products of two functions, one in $x$ direction which is dependent only on $x$ and one in $y$ direction which is dependent only on $y$. These can be solved independently and combined to produce the mode structure. In this way, the 2D waveguide structure can be separated into two single structures, one being a step index planar waveguide in $x$ direction and other in $y$ direction. In fact, this is same as your suggestion for introducing $V_x$ and $V_y$, but in a special way that the solution is very closed to the exact solution
