Replace the existing variable-list with a tree-style variable-selector. allow multiple ways of organizing the tree: file/sweep/variable vs. file/variable/sweep, extract circuit heirarchy from variable names, etc. Perhaps a two-pane tree browser, with the internal nodes of the tree in one pane, and the leaf nodes (variables that can be displayed) in another.
Add icons to the toolbar elements
Enhance use of Gtk2.0 file chooser: wildcards for selecting particular types of files,
Accept drag-and-drop from a file manager to add files, run scripts
Allow drag-and-drop from one wavepanel to another to move wave
Remember/restore the position of the windows, both most-recent-session, and also save it in the scripts.
Add keybinding mechanism
An undo stack for operations that change the view
Add a guile console window, where expressions can be typed to query/manipulate/debug gwave objects and variable data.