FS-UAE can also be built against a system-provided libmpeg2. This is probably easiest in this case. There isn't any configure switch for it, but if you modify configure.ac / Makefile.am slightly, it will probably work:
Code:
diff --git a/fs-uae/Makefile.am b/fs-uae/Makefile.am
index a54a791..eb7990f 100644
--- a/fs-uae/Makefile.am
+++ b/fs-uae/Makefile.am
@@ -1,6 +1,6 @@
# Makefile.am for FS-UAE
-SUBDIRS = libmpeg2
+# SUBDIRS = libmpeg2
WARNINGS =
diff --git a/fs-uae/configure.ac b/fs-uae/configure.ac
index 965b1b3..7781979 100644
--- a/fs-uae/configure.ac
+++ b/fs-uae/configure.ac
@@ -102,8 +102,8 @@ AC_CHECK_LIB([Iphlpapi], [main])
AM_CONDITIONAL([BUILTIN_GLEE], [true])
# Todo: make configurable
-# PKG_CHECK_MODULES([LIBMPEG2], [libmpeg2 libmpeg2convert])
-AM_CONDITIONAL([BUILTIN_LIBMPEG2], [true])
+PKG_CHECK_MODULES([LIBMPEG2], [libmpeg2 libmpeg2convert])
+# AM_CONDITIONAL([BUILTIN_LIBMPEG2], [true])
AM_CONDITIONAL([BUILTIN_MANYMOUSE], [true])
@@ -611,7 +611,7 @@ OPT_FEATURE([FS_EMU_DRIVERS], [fs_emu_drivers], [fs-emu-drivers],
AC_DEFINE([FPU_UAE], [1], [Define to 1])
-AC_CONFIG_SUBDIRS([libmpeg2])
+# AC_CONFIG_SUBDIRS([libmpeg2])
(Not tested, you may have to make some other minor tweaks)