The introduction of Auto-Animate has introduced some problems. The main two arise from objects' opacity being being set to 0% and the fact that objects need to be placed off the artboard in order to create the effect of them moving into place.

In both of these cases, the objects become invisible and in the case of the latter they either interfere with adjacent artboards or the artboards need to be placed far enough from each other to allow for the elements around them, which creates a mess.

The problem of opacity could easily be tackled by introducing a new outline colour in Prototype Mode that highlights invisible objects and perhaps indicates the interaction that has been set on them.

However, the issue with off-artboard assets remains. Therefore, the solution appears either to be a new interface inside Prototype Mode that works in a similar manner to Isolation Mode in Illustrator or the introduction of an Animate Tab, which would address these issues.