This is one of my whackier suggestions, to be sure. However, I think it would vastly improve the flexibility and usabilit of C2 in large-scale projects.
An "inherited layout" is one that shares the charactaristics of other layouts. I would envision it would work on a "tag" system - that is a layer with the same tag as another would be identical, e.g.
<img src="http://dl.dropbox.com/u/1378330/c2InheritedExample.png" border="0" />
This suggestion is to address something I've found when creating a game with many levels. If I make a change to common elements (such as the player's user interface) or introduce a mechanic that require a new object (which then requires a prototype to be present in the level), I must then make that identical change to every layout. This quickly becomes unsustainable when you have 30+ levels, and means I cannot make changes on-the-fly to common elements.
I understand that this is probably not possible, but I think it would be a valuable feature if it is.