"Spotlight" Type Effect?

There are several ways to create a static highlight effect. One way that is fairly easy involves using a full-slide graphic of the flow map. Create the graphic on the slide, then take a screenshot just of the slide (Command-Shift-4). Put one copy of the resulting graphic on the slide background. Cover the slide with a box, and set the box fill to black, adjusting the translucency until the desired dimness is achieved. Put a second copy of the graphic on the slide, and mask out all but the appropriate spotlighted portion (you will likely want to use a circular object as the mask). Make sure that the second copy is aligned exactly with the first (the guides will of course help with this).

To get the effect of highlighting, set a dissolve build for the translucent black layer. It will appear that the image dims except for the part highlighted. You can get more sophisticated by using a Scale Action on the highlighted portion to make it bigger, so that it pops out.

This technique will get you a static highlight, but it won't let you move around a spotlight. To do that, you will have to use a graphics app to create an object mask with a hole in it for the highlighted portion. The mask should be much bigger than the slide. Create the mask so that it is translucent black. You can place this mask on the slide, and use Move Actions to move the hole around so that it appears the spotlight goes along a path. One limitation of this technique (apart from the cumbersome step of using a separate application) is that the resulting mask will not be easily editable, so you will not be able to change the size of the hole on the fly.