4.5.3 has the global ctors bug that causes sketches compiled for MEGA to fail instantly.
http://gcc.gnu.org/bugzilla/show_bug.cgi?id=45263
I also recall a problem with delay(), and an arduino/math.h incompatibility issue.
In general, allowing Arduino to use the system compiler on Linux has caused quite a few issues for Linux users, sometimes because of compiler bugs, sometimes because of bad packaging (mismatched gcc/bin utils/avr-libc)