You can't remove the pull-up resistors for the controller data line. It's an open-collector protocol (just like the i2c) so the two systems (i.e. the gamecube/wii and the controller itself) can only pull down the data line and to set it high they just "leave it" as it is and let the pull-up resistor do its job.If you removed the resistor and didn't use shielded wire, what would noise affecting the signal look like? Dropped inputs, erratic joysticks, etc?