For n=2, the n-dimensional cube is a square, and the (n-1)-dimensional facets are the edges of the square. Replacing the edges with complete graphs on 2 vertices does not change the graph.
There are 3 distinct (under rotations and reflections) acyclic orientations of the edges of this graph:
*->-* *->-* *-<-*
| | | | | |
^ ^ ^ v ^ v
| | | | | |
*->-* *->-* *->-*
Therefore a(2) = 3.
For n=3, the n-dimensional cube is a cube, and the (n-1)-dimensional facets are the faces of the cube. Replacing the faces with complete graphs on 4 vertices gives the graph that is the edges of a cube with diagonal edges added to each face (the "16-cell"). a(3) is the number of distinct acyclic orientations of this graph.