I think the update system got better in later versions although there are sill some usability problems and I am not a big fan of it.

I realize that Eclipse is not for everyone. But a plugin for IntelliJ or some other IDE is a completely different product. FWIW there is a "standlone" version of WireframeSketcher that you can get through Yoxos: http://wireframesketcher.com/install_details.html#yoxos

I'll see what I can do about the immediate edit box. Obviously an option for it could be a solution. I'll see if there are more requests for it.

Take a look at master screens. I think it might be what you are looking for. You can reference screens from other screens and create reusable units this way. Changes to referenced screens are propagated automatically.

I plan to add editing inside groups. I think your idea of logical grouping is good. It was actually this issue that was stopping me from adding the possibility to put in Outline the complete contents of a group. Logical hierarchy would give much more appropriate results.