unfortunately since my ipad is on ios 6 and can no longer be jailbroken there is no way for me to use remoter with an external mouse. of course, even when i could do this the external mice would generally not work very well. It would be pretty cool if you could develop an iphone app that would allow the iphone to connect to the ipad over a wifi connection and act as an external mouse for remoter.
In fact, you may not even need to do much developing on the app side to make this happen. there are quite a few external mouse apps that are already available all that would be needed would be to build in the proper listeners on the remoter app. Here are a few examples:
hipporemote: connects to standard VNC servers and acts as a mouse/keyboard (basically connects to VNC but rather than pull screen images it only connects the mouse and keyboard control). To make this work simply build in a VNC server in remoter.
rowmote pro: this program typically works as a replacement for the apple remote on macs and requires the use of a listening device. the pro version also has mouse and keyboard support. The program has also extended to other platforms and there is a receiver available for jailbroken appletv's so it is likely that the receiver is well documented and the developers may be somewhat helpful.
Ideally of course we would want to be able to use a true physical mouse and this might be possible by developing a dock accessory with a USB port for an external mouse but that would obviously take some development time. the above two options (especially hipporemote) could be implemented almost immediately.