Originally posted by VisualDarkness To the original poster.
The first difference is the working distance from the subject. For the 35mm to get to 1:1 magnification the subject will almost touch the front element. With the 100mm you will have a lot more distance to the subject for the same magnification.
The second difference is the perspective. With the 100mm the things in the background will appear larger than with the 35mm as a wider angle compresses things farther away. The wider lens will capture the scene at a wider angle so more of the background scene will be compressed in compared to the 100mm.
So, I want to +1 to the above two, and then add a third observation....
A lot more distance-to-the-subject can be a mixed bag, a curse as well as a blessing.
If you're trying to photograph something venomous and/or with claws (such as a mother-in-law), then being at a distance may be a blessing.
However, on a warm summers day, the movement of rising hot air may actually cause disturbance in the image - the longer distance-to-the-subject, the more "hot air" will there be between your camera and your subject, and the "more magnification" the more will such movements degrade the image quality.
So, I guess that the LBA answer is, that you will need both