It seems like the mercenary should be able to do basically anything the assassin can do, right? Since the attunement starts only 2 lower than the assassin's... Couldn't i easily do a mercenary/assassin hybrid?
the only thing the class choice does is decide your starting stats and what equipment (and in some cases spells/miracles) you start out with.
the only "permanent" way it affects your character is if your starting class has higher stats in some categories than you need and you never raise them, therefore "wasted" points and a less optimal character.
assassin has higher faith and luck than mercenary, meaning those levels are wasted (unless you want luck for some reason, but currently there's no known reason to want to raise it).
you could use the faith if you built the assassin into a miracle caster, but in that case the int is wasted.
in other words, you should figure out if you want to scale int, faith, or neither, and then pick the starting class that wastes the least.