A common practice is to modify the infill settings in the vicinity of holes where fasteners are going to be attached to parts. It would be nice to have a tool that would do this automatically.
Yes, a way to more accurately estimate the print time would be nice. If you're going to implement this you might as well go ahead and build in some intelligence. Something like a running history of the previous ten successfully completed builds. Take the actual print time divided by estimated print ...
This feature request is already implemented in slic3r. Slic3r allows you to select a different material for the interface layer between the support material and the model. S3D needs this.