Having been using it quite a lot for planning out and taking notes on various things, my wish list is below. I expect some or all of these will fall foul of the simple design philosophy but if you don't ask...

Eddy
- Snap / Grid
I know this has been asked before, and I know you said it wasn't part of the design philosophy but adding an optional 'snap to grid' feature would be brilliant. Align / Distribute are great features, but not really a substitute for very quick and easy accurate placement of note relative to each other as you work.
- Panes
The ability add panes to a map, where each pane is a freely resizable rectangle (and possibly titleable) which contains no text and is transparent such that lines and arrows are visible 'underneath' it. Currently, making a big blank note and sending it to the back hides lines/arrows, as they fall underneath it. This would also be great if each pane could have a custom background colour. Useful for splitting a large map into 'zones' of interest, would supplement the nice existing ability to colour notes.
- Curved lines/arrows
An option to have connecting lines curve around any intermediate notes that they pass through instead of passing straight under them.
- Lock
Such that each note can be individually locked (as opposed to the whole map), which prevents accidental dragging or editing, even if it's selected as part of a group which is then dragged (ie: locked notes within the group would stay in the same place)
- Multiple paste auto select
When multiple notes are cut and pasted, the new copies appear in the middle of the document window and are unselected. If the newly created notes were auto-selected then that would make dragging them all out much easier.
- Intelligent placing on paste
When pasting, would be good if the new copies appear near the mouse pointer instead of always in the middle of the drawing area (which is often already occupied by stuff).
- Hotlinking documents together
The ability to link one map to another (a bit like an HTML link). The name of the linked document would appear much like a link on a website (I think this might be in already? Couldn't figure out how to do it!)
- Nesting maps
The ability to have one map contained within another, such that the 'child' map would appear as a special kind of note, which, when double clicked would replace the parent map. The inspector could be modified to provide 'go to parent' and/or 'go back' controls to navigate back to the parent. (Guessing this falls outside scope - too hierarchical.)