Your version of Fallout3.esm cannot be patched....

[FalloutAddict]

Okay, I'm having the same problem. I reinstalled the game and can't get past this message. I use the Steam version. Tried to install this three times already. Nothing works. I have re-installed re-downloaded. I even went to Games for Windows live and used their version. All I get there are messages that the fo3 esm isn't in the directory. I tried installing in different areas like program files 86, Games folder, external hard drive. All of these were clean installs. Still won't work. If I find a solution I will post it. I first noticed problems trying to use the GECK when converting a fo3 mod. It wouldn't save the files. Then the game wouldn't launch. I worked like 24 hours trying to get it to launch. It was working perfect until the GECK problem. So I tried re-installing nothing works. This is a serious bug and it must me with the new version as this is the only version I have ever used. 

[FalloutAddict]

I was able to get the installer to work. It was a long ordeal. First I had to give up on using the Game of the Year version. To get this to work I had to download everything from Games for Windows Live Market Place. The original Fo3 and all the DLC. Then I had to fight putting these files into an area that would allow me to take the read only attribute out. I could take it out but Windows would put it right back in. The only location I could find that worked was my desktop. So put your fo3 and all its DLC there. Then you need to use the windows live disabler program. However it still won't take the hidden files out so that the installer can recognize them. To do this go to this website and follow the instructions. But you have to delete the leftover files out of their hidden locations or the program will still not be able to recognize them. You have to take ownership of the fo3 folder, the esm, all the DLC. Then and only then will the installer recognize this as a legitimate program.

http://www.moddb.com/mods/fallout-3-reborn-a-realism-mod/tutorials/how-to-find-the-hidden-dlc-esm-files

Last but not least, remember that this website tells you to leave the files after taking them out of their hidden folders. Do not do this! You must delete all these hidden files.

Another option that helps, is to unpack everything like you would for a manual install and then take all the esp/esm/bsa, out of their folders along with a fomod file and add to archive with winRar. Then give it to FOMM and it will process it. This will help clean up any files that get lost during all this manipulation. I had several that were processed but didn't make it into the final install.

Good Luck!