I could be way off base here, but I would guess that most, if not all Chameleon2 users will have Chameleon installed on a partition with Mac OS X installed. That would say that there is an hfs+ partition with a /Extra directory. If that is the case, write the default pointer there.
Or at least most users will have a HFS+ partition where Chameleon is installed in the boot sector. The user-friendliest way would probably be to write to a file on the partition where Chameleon is installed. How safe it is to do this is beyond me.
The problem with saving the selected partition only after boot is that you would need to implement this for every possible OS Chameleon can boot and the user would have to install this script/daemon whenever they install a new Windows 7 Beta etc. So while I agree that this would be the safest thing to do, it would be hard to implement.
If I understand correctly, Chameleon already reads from the partition where it is installed prior to boot. In fact, it must do this to identify the theme to use and read any other key/value sets from the Boot.plist required to control it's current functions.
I think that should mean it could also write to that partition prior to booting a system. If Chameleon could write something to the install partition after the timeout/enter key and prior to transfer of control, wouldn't that avoid the user needing to do anything other than activate the remember option in the install partition Boot.plist?
There is a boot manager on Sourceforge called "Smart Boot Manager". I use it in emergencies like when I have trashed my HD boot sector.
http://sourceforge.net/projects/btmgr/It resides in the boot sector of your HD or on a floppy. It has the ability to boot WinX, Linux and Mac OSX from internal drives or external USB drives. It will remember, if asked, which was the last system started and make it the default the next time the system boots. It allows the user to name each bootable partition. It saves this data in the boot sector where it is installed.
If any of this sounds useful, the source is available at the link I provided.