Go to your Fallout 3 main folder :
...\Steam\steamapps\common\Fallout 3 goty

Rename fose_loader.exe to Fallout3Beta.exe
and Fallout3.exe to Fallout3ng.exe

NOTE : Do not launch with compatibility mode, otherwise steam will not count your playtime.

Now everytime you launch Fallout 3 : FalloutLauncher.exe -> Fallout3Beta.exe -> Fallout3ng.exe
Don't ask me why rename it that way. It just works