I am assuming you are referring to Prezi. I agree that Prezi is one of the worst presentation software out there. Both presenting, viewing, and creating one of those presentations is the worst.
I think the main issue with Prezi-style presentations is that it demands too much skill to use properly. A better interface with sensible defaults and much less emphasis on wow-factor would help a lot here.
Normal powerpoint "only" requires a basic awareness of composition and narrative coherence, which already is too much to ask in practice. To make good Prezi presentation you need to have the skills of a cinematographer/editor. Specifically, the skill of continuity editing[0] so your audience can follow what is going on.
What we want is the calm, easy to read compositions of, say, Yasujirō Ozu or Wes Anderson, and Akira Kurasowa's sense of movement[1][2]. Instead everyone uses it in a way that it feels more like the worst aspects of Bayhem[3].
I still believe Prezi-like presentation tools have the potential to be good, because they could be used to map relationships in your narrative to spatial relationships. But that would require a) that you are aware of those relationships yourself and b) that you posses the skills to translate that into spatial compositions that are coherent.
This is obviously an unrealistic demand, so instead the tools should assist you with that. It needs is an interface that helps users structure their story, with sensible default conversions. Maybe something like Treesheets[4], where you can create a tree-based hierarchy in your topics, and then a conversion of that to a spatial hierarchy that is easy to follow, and not a distraction from the actual narrative.
The vertical slides in reveal.js are a step in the right direction, starting from the powerpoint side of the spectrum[5]. What we need a step in the right direction of the free-flowing Prezi side of presentations. At some point there will be a happy middle ground.
EDIT: Maybe we should all just work our way through Pixar's storytelling course on Khan Academy[6]
