Reasumming this discussion we could make two control schemes:
-Scheme 1:
LMB - A item use
RMB - B item use
Ctrl+LMB - A item throw
Ctrl+RMB - B item throw
Shift+LMB - A item secondary use
Shift+RMB - B item secondary use
And for people with four or more mouse buttons:
-Scheme 2:
LMB - A item use
RMB - B item use
3MB - A item secondary use
4MB - B item secondary use
Shift/Ctrl+LMB - A item use
Shift/Ctrl+RMB - B item use
Or we could just use the first scheme with third and fourth buttons ALSO be secondary use...

>With the system we currently have, this would suggest a Clonk can have more than 2 arms.

He might just switch to the other item automatically when using it.

I'd really like to see more possibilities on jumping behaviour. The player should have the opportunity to vary the intensity of jump height, e.g. by pressing the "up" button for a low jump and holding it shortly for a higher jump.

Also I'd really like to see more possibilities on one-on-one fights using sword/club and shield. Blocking with the shield should not block every attack, but block depending on how your opponent attacked you. Let's see how Street Fighter works here. Blocking will block normal attacks and attacks from the air. Duck-block (holding "down" button while blocking) will block normal and duck attacks. Maybe adding some simple special attacks (e.g. pressing [down] [forward] [attack] for a somewhat stronger hit).
Don't know if that goes a bit too far away from original Clonk fighting, but it would surely give the game more depth.

The current controls seem to be made for short full-of-action rounds, the longer ones seem to loose here (using the mouse always for almost every little thing, in a round that takes ours, could be very annoying). Little "thingies and buttons" and stuff are not a common thing in videogames and yes there is zoom, but always zooming seems to be annoying too (you understand what I mean?). To be accurate with the mouse like with the keys while digging an other things is really something else.
Even though I don't think it's possible anymore, there should be a way to play without mouse, or at least a way to do many stuff without. Somebody might say, "I'ts usual in any videogame today to use the mouse for almost everything", yes but there are not so many 2D Jump 'n' Run styled games where it is so.
Perhaps it's just the fact that I have to get used to this kind of control, but to dig with the mouse like it's right now, is really strange to me (other stuff too).

Ah btw: make the mouse cursor tiny as possible, just a few pixel large, just for practical reasons, because it's much easier to point at things correctly then, and with controls like the current it's very important (I think you know what I mean).