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You already can create your own team for the Master League in PES 2011.
If you go in to edit mode you can simply edit any unlicensed team, place them in whatever league you like, and use them for the Master League.
It's not the same, I used to love creating my own team, having a budget of like 1000 points to buy 2/3 players, and changing the club kits regularly and making special ones for cup finals, the glory days.