Hello,
I think it would be very usefull to implement a layer system like in Photoshop or Gimp.
It could improve maintenance and fragments so much !

I do a lot of presentations with slides, on i always think "well, it's great, but it absolutly need layer".

The main idea would be to allow user to create multiple layers on the same slide and select the one he want to see on work on by some checkbox or something like that, re-arrange layers order, etc.

All the interest of this would be to animate layers by using them like fragment and play fragments like this :
1 - Show Layer 1
2 - Show Layer 1 fragment 1
3 - Show Layer 1 frag 2
4 - Hide Layer 1, Show Layer 2
5 - Show Layer 2 frag 1
6 - ...

This way we can absolutly keep horizontal separation (like i do a slide about CSS, then a right slide about HTML), vertical separation (like inside my slide about CSS i do a slide about text formating, then, vertically a second slide about block formating).

And add a better way to manage on-slide separation (like inside my CSS -> block formating part, i can do a layer about block, another layer about inline, etc.).