It's very surprising that exporting an FBX results in just a single animation clip containing the entire timeline. Unless people are really creating one iClone project per individual animation, a far simpler workflow would support labelling portions of the Timeline, such that labeled regions each map to a separate animation clip in the exported FBX.

We currently have the "Collect Clip" track, which allows the drag-selection of a region for exporting the motion. However, the selected region isn't permanent. I'm picturing a similar track where users can specify the name they want to assign to the animation clip, such that the exported FBX will contain an arbitrary number of animations, one per label. (Similar to the way Audacity, for example, allows regions to be labeled, resulting in one exported audio clip per label.)