Ignoring the "getting in your own light" thing, the longer lens is nicer for situations where you cant get "truly macro close" to your subject.
Fish or insects in an enclosure, and in certain situations flowers are great examples.
I wish I had a 200mm macro, or at the very least 180mm I REALLLLLLY wish I owned & brought one of those instead of my 90mm when I went to Longwood gardens earlier this summer. The 90mm was fine for the majority of the day, but a longer lens would have been totally welcome for shooting the lily-pads. In hindsight, any long lens that focused closer than 9 feet would have been adequate for the lily-pads, but it never hurts to kill 2 birds with one stone.