Make mouse left-handed and touchpad right-handed

I understand your frustration, but this problem can be solved very simple with the help of xinput tool.

First plug in your USB mouse, then run the following command:

xinput list

to see the id of your mouse. The output of above command it can be similar to:

xinput | cat
⎡ Virtual core pointer                      id=2    [master pointer  (3)]
⎜   ↳ Virtual core XTEST pointer                id=4    [slave  pointer  (2)]
⎜   ↳ SynPS/2 Synaptics TouchPad                id=14   [slave  pointer  (2)]
⎜   ↳ USB Mouse                                 id=11   [slave  pointer  (2)]
⎣ Virtual core keyboard                     id=3    [master keyboard (2)]
    ...

In the above example the USB mouse has id=11. We will use this id in the following command which will swap buttons to be left handed only for the USB mouse (and not for tauchpad):

xinput set-button-map 11 3 2 1

In general:

xinput set-button-map id 3 2 1

To revert the change, use:

xinput set-button-map id 1 2 3

To make the change permanently, add the following command at Startup Applications (search in Dash for Startup Applications):

sh -c "xinput set-button-map id 3 2 1"

Update:

Since the id might change after reboot but the name of the USBmouse not, you could also grep for the name of the mouse and apply it. To skip the details reg. picking out the name the final solution looks like:

for id in `/usr/bin/xinput list | /bin/grep 'USB Mouse' | /bin/grep -o [0-9][0-9]`; do xinput set-button-map $id 3 2 1; done;

pack it into the above mentioned Startup Applications you'll get finally:

sh -c "for id in `/usr/bin/xinput list | /bin/grep 'USB Mouse' | /bin/grep -o [0-9][0-9]`; do xinput set-button-map $id 3 2 1; done;"

There's an even simpler way than in Radu Rădeanu's answer. xinput accepts the name of the input device as an alternative to its numerical ID. Since your USB mouse is probably treated generically, it's name is most likely USB Mouse. Therefore you likely don't even need to run xinput list.

Thus your xinput set-button-map, with this name in place of the numeric ID, becomes:

xinput set-button-map "USB Mouse" 3 2 1

This takes the place of xinput set-button-map id 3 2 1 and should achieve the same thing, with 3 2 1 making it a left-handed mouse, just like when the numeric ID way is used. (And replacing 3 2 1 with 1 2 3 will still work to switch it to being a right-handed mouse.)

This has the advantage that, provided it works initially, it will continue to work across reboots, without having to obtain the device's ID number using long, complex commands.