Well, FFII doesn't have any optional side-quests (except for the extra dungeon in the Dawn of Souls version), so I'm not really sure what a 100% Completion would be. Maybe getting 100% of the treasures in the Bestiary, and maybe encountering 100% of the monsters in the game. Mastering all weapons, all spells and all stats for every character is totally unnecessary and takes forever to do (if it's even possible since I think FF Origins still has the feature of weakening stats).

Now that I said it, though, you wanted some advice, so here's a tip. Don't try to make your party members jack-of-all-trades characters who are excellent in every way. The game mechanics have been designed in a way that they favor specialized party members. Make someone a white mage, make someone a black mage, make someone a fighter, but don't try to make someone a juggernaut that can do all that him/herself. Don't give the mages powerful weapons, shields or heavy armor because that will cripple their magic.