use --prefix=/usr on the configure script
/usr/include is managed by the system (apt, yum, pacman, portage, zypper or urpmi depending on your distribution). /usr/local is not managed, it host files that are outside of the main managed tree. It is not recommanded to override things in the managed tree, it cause problems in the long term. Why don't you just use the SDL developper package provided by your distribution?
sudo apt-get install libsdl-dev