Hi mmagg,
I have experience with mechanical desktop, so in inventor I suppose it can only get better. I experienced no problems importing IGES to Ansys from mechdesk, however there are some general guidelines to prepare the geometry.
I like to export wireframe (2D or simple 3D) or surface model (complex 3D) and mesh it in Ansys. The surfaces must be closed and trimmed. Sometimes you can find some bugs, then you unfortunately have to recreate the critical surfaces either in Ansys, or in Inventor and import the whole thing again. You should not exceed (or stay below) the number of edges defining a surface what Ansys can work with at meshing (arcs, cylindrical objects can be tricky). You might have to adjust the IGES tolerance values to less sensitive at complex geometries, this has usually no negative effect since the mesh will coarsen your resolution anyways.
Hope this helps
GSC