I can
apt-get remove mypaint mypaint-data
(or
apt-get remove mypaint
apt-get autoremove
)

rm -rf ~/.mypaint

And then install it
apt-get install mypaint

It will create ~/.mypaint on the each boot, so it can safely removed.

Sometimes it reboots whole phone, specially when starting and stopping it on the loop (=debugging starting)

Color Picker is not fully workable, ctrl might be used on the same purpose. If color-square doesn't hide after ctrl+click, press 'r' and it should be gone. This will be fixed when some skilled python-gtk developer step in. (Or this might be issue of too old pygtk on the phone)

If it doesn't start there are something wrong with dependencies/libraries (missing modules). I just do not know what. When this it solved, we have valuable information.