Transitions are the fancy visualizations that take place when you move from one slide to the next. However, not all transitions on the Mac OS X version of Keynote work on the iPad version. Of the bunch, most are text- and object-effect oriented in nature, such as the "shimmer" and "sparkle" transitions. However, they also include the "revolving door" 3D effect, and "fade through color" and "wipe" 2D effects.
If the plan is to start your workflow on the Mac OS X version of Keynote and use your iPad as the actual presentation device, consider using other transitions.
Builds and Actions
If transitions are individual trees in your presentation forest, then builds could be the branches on each individual tree. Builds refer to the behavior of elements coming into or out of a slide. For instance, on the first click, Steve will reveal a picture of a Motorola 68k processor, one object on the slide. Then, on his second and third clicks, he'll bring up an arrow (click 2) pointing to a PowerPC processor (click 3).
As is the case with transitions, presentations with the shimmer, sparkle and wipe builds are incompatible when opened on the iPad version of Keynote. In addition, other notable incompatible builds include squish and convergence.
While you can substitute one build for another, finding a workaround for actions may prove trying. Actions are a slight twist on builds, allowing you to customize motion animations for objects on the screen: for instance, an airplane traveling to different parts of a map upon a click. If your presentation is highly action dependent, you may be better off just using your Mac.
The Mac OS X version of Keynote allows you to build a variety of charts in both 2D and 3D. However, the iPad version only supports 2D charts; 3D charts will be converted into 2D when the iPad imports it. However, all other style aspects of the chart are largely intact when imported. For instance, the Mac OS X version of Keynote allows you to set a color or stylistic options for your chart. In my tests, all 3D and 2D image and color image fills carried over.
Themes and Fonts
Themes, even those not included on the iPad version, also import over without much lost in translation. However, if the theme contains fonts not present on the iPad, a substitute font will be used.
And that's the case with all fonts not present on the iPad. However, there is a workaround: Padilicious's "Render Text to Image" service. As its name implies, Render Text to Image allows you to convert any text into a PNG image via the Services menu on Mac OS X.
Shapes and Grouping
There's no need to get bent all out of shape about shapes. All of them, even custom drawn shapes, carry over without a hitch. However, if you plan on grouping your shapes or any other object in your presentation, these groups won't be treated as such on the iPad. This means that each of the objects of a group on the Mac OS X version of Keynote will be treated as individual objects, rather than one object.
While the iPad version of Keynote lacks some of the features of its Mac OS X sibling, it doesn't mean that it's unusable. It's a fairly robust app that, with a little tweaking on your part, can be just as useful.
However, no app can compensate for a presentation that is lacking in preparation and thought. To be fully prepared for your presentation using your iPad, make sure that you buy, and bring with you, your iPad Dock Connector to VGA Adapter. Otherwise, there may not be a presentation.
Also make sure that you're fully well-versed in your material - its content, transitions and builds. Keynote for iPad, unlike the Mac OS X version, does not have a Presenter Display option. This means that you can't look at notes for the current slide and peek into upcoming slides and builds.