You can do any version, and it's only to Neo Ex-Death. So you don't have to do the bonus bosses or the bonus dungeon.
People beat the game with only one class the entire game. Hell, I just finished watching a LP where someone beat the game (and bonus dungeon) at L5/4/4/4.
It's really not that bad, especially if you just do regular. Hard might actually be easier if you get something like two Knights or whatever, but it's a bit chancey.
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Current Let's Play: Legend of Mana
http://forums.somethingawful.com/showthread.php?threadid=3474994