From page 107 of the Keynote User Guide:
Tips for Creating a Magic Move Transition
Magic Move doesn’t work with tables, charts, or movies.
For best results with a Magic Move transition, duplicate the slide and apply the Magic Move transition between the original and the duplicate.
To set up a Magic Move transition:
1 Create a slide and place the objects (text, shapes, images) where you want them.
2 Select the slide in the Slide Navigator and press Command-D to duplicate the slide.
3 On the copy of the slide, reposition and resize some or all of the text, shapes, and images on the slide.
4 Add any additional text or graphics you want to add to the copied slide, and delete any objects you don’t want on it.
5 Select the first slide of the pair and apply the Magic Move transition.
That being said, there are a lot of little tricks. For example, you can usually group objects to exclude them from Magic Move matching, and if you have an object that isn't matching between slides, usually deleting it from the second, copying it from the first, then pasting it onto the second will match them.
Do you have specific examples of Magic Move not doing what you want it to? If so, we might be able to help you out.
(And if you want Apple to know about it and hopefully fix it in the next release, you could tell them what isn't working for you via their feedback form, or—to be ESPECIALLY helpful—file a bug at
http://bugreporter.apple.com and attach the misbehaving Keynote decks to those bugs.)
