As you say, the .obj format supports n-gons, but not holes in polygons.

I think exporting quads would be a good solution for the quality of the exported object and compatability to most softwares. (Some softwares, like z-brush, have equaly large problems with tris as with n-gons)

My major problem with the export at the moment was the inability to use the quality slider, it was non operational/stuck on few polygons.

(Like it's described in this post: http://moi3d.com/forum/index.php?webtag=MOI&msg=137.5 )