I know the advantage of magic missile vs thunderstomp is that magic missile does damage and thunderstomp does not, but thunderstomp will treat your caster level as BAB so your to hit will be better.
Some ideas which may or may not work all together.
*Greater thumberstomp will do this against all creatures in the area, you actually would need to find a way to exclude your friends.
*If you are human, you may want the bred for war trait, which would give you a +1 on the trip attempts.
*vicious stomp. Every body that falls prone next to you triggers an attack of opportunity...
*Kobold groundling: everybody prone is denied its AC against you... You could sneak attack with that vicious stomp