Time. They introduced a whole new mode to Madden. Since Madden is a yearly title, they at the time likely realized that the pros of developing a brand new mode with new features outweighed the ability to edit players. I'm also guessing they would have LOVED to implement player editing with the new CCM and XP features, but simply did not have time to properly tune the logic to do so. It will probably be in 14.
Love it or hate it, Madden being a yearly title makes it difficult to innovate without sacrificing old features. ESPECIALLY since Playstation/Xbox have limited resources to work with. Making cutting even more necessary. I would guess that if Madden was PC-only, they would be able to do much more.
They work within the limitations of an extreme time-frame (yearly) with the additional limitations of having to cater to the limitations of console resources.
I wish Madden would just come out every two years, with a 10 dollar paid roster update for the between years or something. That way they could have the time to develop an innovative title with fewer "cons".
But that's just me.