It's due to the issues with FA Premier League licensing rather than solely 'club' licensing. I'm sure EA and FIFA will have exclusivity of the Premier League license with the FA, as a condition in their deal - which Konami can't really do too much about.
The UEFA Champions League license is completely separate to that of the FA Premier League license. At least Konami have secured the former, which never used to be the case years ago. Konami just can't afford to compete financially with EA, so as long as they focus primarily on nailing the gameplay, then they have a great chance of propelling themselves into a position to purchase the rights to licenses at some point down the line. Fortunately, this year, Konami has managed to cook up some really exciting and addictive gameplay, which is the most important aspect for me.
I'll be getting the game for Xbox 360, so all of the editing options will still be available to me, along with the gameplay too. And given that it'll be cheaper also, it's a win/win in that respect.