Several companies like Experian are trying to get around FICO by coming up with their own systems. They pitch it to the same clients as FICO, so some buy on, some don't. It makes business sense, Experian, TransUnion collect the scores but then FICO aggregates and makes money on that. So trying to cut out FICO would increase margins at Experian since they already own the data.
I wouldn't put too much stock in any of the free credit sites in terms of score. For the actual report/inquiries/etc. they do have value. My brother worked at FICO for several years; they spend a lot of time crunching numbers and refining algorithms to keep their score accurate and relevant. If it ever becomes unreliable, FICO is done. So as people and trends shift and/or people try to game the system, FICO does adapt. I forget the statistics, but FICO scores are surprisingly accurate especially when it comes to stuff like instant credit checks for cell phones/store cards/auto loans.