You can edit the wizard files of Qt Creator. The files are in the following directory:
Qt-Dir/Tools/QtCreator/share/qtcreator/templates/wizards/
If you look at the directory there are some folders related to different wizards. For example if you look in to the "plaincppapp/qmake" folder, there you can see a "project.pro" file which is a template pro file. You can just edit that file like:
TEMPLATE = app
CONFIG += console
CONFIG -= app_bundle
CONFIG -= qt
CONFIG += C++11 #added this line
SOURCES += main.cpp
Next time you create a project by that wizard, your custom pro would be created for the project.