I made VLC.app as best I understood your instructions, but the result was the same, no gui:
$ make VLC.app
make: `VLC.app' is up to date.
$ make VLC-dev.app
rm -Rf VLC-dev.app
cp -R VLC-tmp VLC-dev.app
/usr/bin/install -c -m 0755 ./bin/.libs/vlc VLC-dev.app/Contents/MacOS/VLC
ln -s -f ../../../modules VLC-dev.app/Contents/MacOS/plugins
$ ./vlc
VLC media player 2.1.0-git Rincewind (revision 1.3.0-git-5381-gecfe166)
[0x7fc183c0a6e0] main libvlc: Running vlc with the default interface. Use 'cvlc' to use vlc without interface.
[0x7fc183c90af0] [cli] lua interface: Listening on host "*console".
VLC media player 2.1.0-git Rincewind
Command Line Interface initialized. Type `help' for help.
>
Could it be that my configuration is just not finding Qt4? config.log includes the following:
ENABLE_QT4_FALSE=''
ENABLE_QT4_TRUE='#'
dnl ...
HAVE_QTKIT_FALSE='#'
HAVE_QTKIT_TRUE=''