Sorry, I don't mean to say that it's insignificant - clearly it matters a lot to you. However, you mentioned that there would be problems for "all but the most basic" of presentations and that you have a "long list." I do some complex things with my animations and graphics, but as I mentioned before, I'm still fairly new to using the iOS version of Keynote with my OS X presentations. I haven't noted any issues, but I'd like to be aware of them in order to avoid at all costs having them pop up during a live presentation.You brush off the custom font issue because you don't use them.
If the only issue is fonts then I don't mean to say that it's insignificant, but it doesn't affect those of us who don't use custom fonts. If you had anything else that you've noticed, I'd be very interested to hear it.