USB is by far the most configurable choice through the Trident prefs of the excellent Poseidon USB stack.
However when CPU load gets high, the USB ports are affected far more dramatically than the Amiga's mouse port. So you will get jerky operation with high CPU usage. Another disadvantage is that you can't use the USB mouse for the Early startup menus (not a major issue).
Having said that, I have been using the
Logitech MX1000 USB Laser mouse with Poseidon USB+
Spider for over a year and it is very smooth and high quality.
Here is what it looks like when you configure the mouse in Poseidon. Note how you can assign every mouse buttons to actions if you wish.
http://www.amigakit.co.uk/images/poseidon-mouse.jpgAFAIK Posedion does have ability to allow the Posedion stack to stay resident after a warm reboot, but I haven't attempted this. This may allow the Early-Startup Menu to be used with the USB mouse. On the very rare occasion I go into the Early Startup, I generally use the AMIGA+Cursor keys to navigate anyway.