Apple Thoughts: Apple Feels Your Pain About Keynote for iPad

"Apple's iPad-ified iWork apps are generally praised for their polish and functionality. But one place these apps, particularly Keynote, can fall short is when opening a document imported from their desktop counterparts. Specifically, importing a Keynote presentation can often strip critical data out of the document."

So that is a definite problem but Apple has some help for you in their support document called "Keynote for iPad: Best Practices." They have a variety of recommendations including slide size, fonts, slide types and image formats that won't get "lost in translation" when importing to iPad.