Standalone OpenCV

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Apparently, the CMake "find_package scripts" for OpenCV installed by ROS rely on their own path to find OpenCV:

# Extract the directory where *this* file has been installed (determined at cmake run-time)
get_filename_component(OpenCV_CONFIG_PATH "${CMAKE_CURRENT_LIST_FILE}" PATH CACHE)
set(OpenCV_INSTALL_PATH "${OpenCV_CONFIG_PATH}/../../..")

If you use your own FindOpenCV.cmake instead, you should be able to find your actual OpenCV installation without relying on hardcoded values in your CMakeLists.txt.

You can try to get a generic FindOpenCV.cmake (maybe this one), put it in your CMake modules directory, and then (before calling find_package):

set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/path/to/your/cmake_modules/directory ${CMAKE_MODULE_PATH}) 
find_package(OpenCV REQUIRED)
...
target_link_libraries(foo ${OpenCV_LIBS})

Note that you need to make sure that the first FindOpenCV.cmake CMake finds is yours, else it will fall back on ROS' OpenCV. You can check this Stack Overflow post for more information. The rest depends on your FindOpenCV.cmake, you just need to read the documentation at the beginning to see the variables that may need to be set.

Another solution would be to use pkg-config if OpenCV 3 is installed with pkg-config support.

# You can set PKG_CONFIG_PATH if opencv.pc is in an unusual location. Note that pkg-config will
# look for opencv.pc in all the directories in this path, and stop at the first opencv.pc file found.
# You can probably try something like:
# set(ENV{PKG_CONFIG_PATH} ${OpenCV_DIR}/lib/pkgconfig:ENV{PKG_CONFIG_PATH})
find_package(PkgConfig REQUIRED)
pkg_check_modules(OpenCV REQUIRED opencv >= 3)
# OpenCV_FOUND: OpenCV found on the system
# OpenCV_INCLUDE_DIRS: OpenCV include directories 
# OpenCV_LIBRARIES: libraries for linking in order to use OpenCV
# OpenCV_LIBRARY_DIRS: OpenCV library directories

If you have both opencv.pc installed (one for OpenCV 2, one for OpenCV 3), you may want to rename OpenCV 3's file opencv3.pc, and use pkg_check_modules(OpenCV REQUIRED opencv3) instead. You could also use this pkg-config method and put that in a FindOpenCV3.cmake script (e.g. this script that can be adapted easily).

I suspect you're going about this the right way by manually specifying include and library directories. It won't be portable or installable elsewhere, but it should get you off the ground and allow you to experiment with OpenCV3 on your own system.

My best guess is that the search paths are getting passed to the compiler in the wrong order, and it's searching the ROS include path before the opencv paths that you're specifying.

Try moving your include_directories() and link_directories() statements as far up your CMakeLists.txt as you can; preferably before your find_package(catkin ...)

It may also be worth running catkin_make with VERBOSE=1 so that you can examine the exact arguments that are being passed to the compiler and the linker.