Some ideas that I think might work:
I would like to see mouse scrolling. Push the mouse to the edges of the screen in full-screen mode, or click and drag to pan.
Clickable mini-map for instant jumping around.
Perhaps a left-click on an unknown underground tile should designate it for mining by default, while clicks on trees and herbs should designate those for chopping. Actually make that a toggle (so click again would undesignate).
I think some things could be consolidated a bit: stockpiles and zones could probably be the same menu. Meanwhile, construction and digging are sort of similar, but slightly different processes to these. It would be good if they were all consistent with each other, so that once you've learned it once you know what to expect for the others.
Scroll-wheel zoom would be nice as well, but I suspect that's a bit much for the moment, so probably bind the scroll-wheel to Z-levels or lists by default.
I'd also like to see a sort of stockpile summary, showing what it contains at the moment.
The string-filter facility which was recently added to the dwarf language name selector is excellent. It be useful everywhere else we have lists of stuff in text.
Left-click: context sensitive left-click action.
Left-click-hold-drag: selection box?
Right-click: context sensitive menu pop-up.
Right-click-hold-drag: pan the map.
Or, i've you've selected an action or mode to use (designating stuff excetera), then:
Left-click: perform action here.
Left-click-hold-drag: perform action in an area if applicable, otherwise ignore the silly user.
Right-click: cancel mode or action.
Right-click-hold-drag: pan the map.
And have a sort of context priority to decide what gets selected/menu opened in case of conflict:
1) Your creature
2) Enemy Creature
3) Item on ground or in stockpile (but probably not in normal room).
4) Room/stockpile (since creatures are usually smaller than rooms).
5) Trees/magma/water/whatever.
6) Tile
Actually, this has given me another idea: hyper-link like behaviour. Suppose you've left-clicked to view a tile? Perhaps the things listed in the tile view should also be clickable to select them for viewing.
With most of this, auto-pause functionality probably wouldn't be helpful. Perhaps instead reserve one key to pause/unpause in any situation, and do nothing else.
Edit: while I'm having a bit of a brainstorm...
Some sort of view mode for the mouse while nothing is selected, so that whichever tile it's over is displayed.
This then implies we need a way to unselect stuff, but I've already used right-click for context menus, and you can't left-click off anything because the played might want information about anything, so every tile will have something you can select or do. Gah, don't know how to fix this.
Right-click context menu should always include 'help' at the bottom.
Might be some use for double-clicking, e.g. pull a lever.