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Well, I will point out one thing for you. The two extras are the Tomoyo route (not Tomoyo After) and the Kyou route. Since both of those were romance routes, they are mutually exclusive to each other and to Nagisa's route. Thus they were seperated while keeping Nagisa's route since her's is the only one that leads to After Story (the generally accepted great part of the series).
For the rest. Eh. To each their own.
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