I think the second would be confusing because of the tabs used for multiple files.
On my side, I was suggesting that : http://www.arduino.cc/cgi-bin/yabb2/YaBB.pl?num=1266171915#5
Being able to select the programmer setting (bootloader, usbtiny etc) of the preferences.txt file from the Menu. That menu could be hidden and shown if you check a box of the preferences so that it doesn't confuse the newcomers.
Or even better: profiles that allow to give a board a name, a type, a port and/or a programmer. The last profile setting used with a sketch could be stored in the file itself.