Even with new pilot code there are platform issues that have to be dealt with. SDL for instance uses mouse buttons 4 & 5 as the mouse wheel (up and down, respectively), whereas Windows treats the mouse wheel as an axis. It can still be done with some hacks to the Windows code to make it see the mouse wheel as buttons and then have the extra buttons be 6 and up. The easiest thing would probably just be to wait until the Windows side of things moves to SDL and then there won't be any weird hacks involved to support all mouse buttons and the wheel.
There is also an issue of the mouse and joystick buttons overlapping as far as the control code goes. These will need to be separated before any real changes can be made to support additional mouse functionality.
Either way, the new pilot code is set up to support this, so it will all be ready once the rest of the code is changed to properly support the mouse.