Thanks for the input, guys!
Highlighting the pathing is a must.
Fortunately Cogmind already does this!
But, it's off by default because it pretty much has to be--you don't want that snaking line staring at you constantly. It looks terrible.
Hold Ctrl-Alt for path highlighting.
As you suggest Cogmind does not have movement logic that changes drastically, so this feature isn't an absolute requirement, especially because when there are hostiles in sight, you can't even path to your destination at all! (Movement is handled one cell at a time in this scenario.)
Access to every command with only one click is ideal.
Right and left mouse can be assumed, but they shouldn't be when possible. Mouse wheel should never be used for frequently used precision commands like wait. The difference between 3 and 4 rounds can mean the difference between getting your weapon blown off.
Context sensitive commands are nice and all, but forcing fire is vital for anybody using explosives.
Every command is accessible via mouse, but there are so many it could take a little while to learn them.
Mouse wheel is just a secondary input option for waiting, while there's also '.' and 'numpad 5'.
As for another pure mouse method of doing it, you do mention an alternative window in which you could access buttons, but making one of those much more important than the others for a large group of players might imbalance that part of the UI. That's an interesting idea, though I would think that would also be a really slow way to get much done.
The only way I know of to order a unit involves the keyboard.
There's a console specifically dedicated to ordering units purely via mouse clicks: F6 Allies control console. There are three ways in all to issue orders: The keyboard 'o' method, shift-RMB on map for context sensitive menu, or left-click on the ally listed in the Allies menu (again, F6). Or are you referring to something else?
Hover-text is absurdly handy.
The scan window is great, but it separates the information from the location. An option to have names appear on hover would be great. I understand there's a boatload to visually parse already and scanning over things would be annoying, so I suggest a user-definable wait time.
For mouse users, precisely because as you describe it could be really annoying and cover up content, this is accessible only with keyboard modifiers: Hold Ctrl-Shift.
There is an option for the hover text to appear when using keyboard mode under "Options" -> "Visualization" -> "Auto-label on examine", but I've just noticed it doesn't work when mousing over items. This would be a good addition to the mouse functionality.
This was intentional, because in practice it's more annoying when mousing over them (for me), so I decided to make it accessible only on demand. I could add an option to make it always occur, for those who aren't annoyed by it.
For mouse use, I made the decision that the UI is so full of features that it will be pretty much impossible to control secondary features purely via LMB/RMB, so I consider the requirement to use Ctrl/Shift for optional features within the realm of "normal mouse use." The other solution could be to add, but I rather dislike what that would look and play like...
Minor tidbits
That ? in the corner of the screen is so small I needed a magnifying glass to notice it existed.
I was thinking about making that one bigger when I get a chance. It's currently using the text font rather than the map font. I'll probably be switching it over, but at the time I was trying to keep it consistent with the other buttons.
This last one isn't a mouse gripe, but your log window doesn't display its binds. L/A/I/C should really be F5/F6/F7/F8.
It displays them in help mode, which is the purpose of that mode. I prefer the idea of using abbreviations for what they actually do rather than their binding, because seeing "F5/F6/F7/F8" doesn't remind the player at all what they do, while as soon as you learn that those letters are mapped to F5~F8 in a row, you both know what key to hit for each one
and have a clear representation of what each window is for.
(Sorry for the very direct responses--trying to take care of a lot of stuff here very quickly...)