Suggestions:
Perhaps the ability to change the "chop size." This is basically how large/small the subdivisions on a given face are created for the purpose of illumination. Large chop values result in stair-stepping lightmaps, but are faster to render.
Also a variable lightmap smoother so you can configure how sharp a shadow should look.
Eventually, switchable lights. You'd have to break the lightmap up into sectors and render all the possible outcomes of light switching in a given sector.
Ability to add "fake faces" so that you can cast shadows to areas that shouldn't normally recieve a shadow; don't import these into the final model, but just use them to determine the texture illumination.
Little things, like the ability to adjust the global lighting scale, RGB gamma, cutoff values for rendering lighting of 0 luminosity (like anything under 10 will recieve a 0), ambient lighting (as a vector: direction, intensity, color).
Hope these ideas help... I look forward to seeing you develop this project!