Since you are committing for a perfect game, here are a few suggestions that you should keep in mind:

• 100% Achievements: You can complete all achievement in the second playthrough. However, it's going to be very hard to defeat Proto-Babil, so it is recommended to max out all stats in the third playthrough before confronting Proto-Babil.
• Rare item: Do not attempt to farm any rare items before getting Treasure Hunter Augment. Well, for example, if you spend 10 hours hunting Bomb Summon, it's 5 hours with Treasure Hunter. I hope you get it and you don't want to know how frustrated it is to farm those rare items (they are very rare), but you have to do it for achievements.
• One time entry: There are some areas where you can enter once, so make sure that you kill all types of monsters within the area for Bestiary.
• Notice: Pay attention to the notes "Unequip", it means that one of the member will leave the party soon. (monster) means that there are monster inside the chests.
• maxing stats: If you want to max stats for all characters, you should follow this guide how to distribute augments for the final five, but you must give a specific numbers of augments to other characters to get all augments. For example, you must give Fusoya 2 augments to get Phoenix, Omnicast, and Bless from him. 
• New Game+ Carry Over: Onion Equipment, Adamant Armor, Tails, Apple, Soma Drop, augments, map completion, and hidden summons.
• Apple and Soma Drop: Do not waste your Apple and Soma Drop in the first and second playthroughs as you can only max all your characters' stats in the third playthrough. 
• Play style: how you like to rearrange your party and how you setup for boss fights are completely up to you. There are some bosses you may find them very difficult to defeat so I wrote some notes along the way. Make sure you read them.