I think Owen's dubious win benefited heavily from United putting the English league back in focus by winning the CL. It was also on the back of that win that it started to solidify itself as a back among the top 4 leagues and was just generally becoming ever more marketable.
Beckham and other united players during the treble season were held back by the league being seen about on par with the current french league at the time, it was 6th in the coefficients. A great season there just wasn't seen as worth nearly as much as Italy or Spain.. imo Shevchenko was individually the best that year in CL.
There's been a lot of years where more than one or two players would have been worthy. I'd prefer seperate awards for Goalkeeper, defence, midfield and forwards. It might be harder to decide at times where some players best fit, but it would be of more historic value in showing each year/seasons best in a more varied way than boiling everything down to one player.