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Recently I restarted Etrian Odyssey 3 with new characters and have managed to make it to the Deep City fairly quickly, but now I have the problem with giving my characters subclasses. Any advice?

Prince
Monk (Book user)
Gladiator (Club User)
Farmer
Zodiac

I haven't unlocked Yggdroid or Shogun yet, so I can't use those, it would be helpful to know which is more useful.

Shogun.


[spoiler]Shogun[/spoiler]

Shogun - As a main, they're relatively brittle due to sacrificing an Armor slot for a Weapon with Second Sword. Worth mentioning now that Second Sword does not change your skills, it merely grants you an extra weapon for regular attacks. There's only one skill that changes directly due to Second Sword but more on that later. Their brittle stature, though, is irrelevant most of the time due to Line Guard/Guard Order/etc.

Offensively, they only have two really noteworthy attacking skills: 5-Ring Sword and Warrior's Might.

5-Ring Sword is basically Nine Smashes but without the Accuracy penalty and with an additional hit (same damage per swing); though, it only does the 2-10 hits for a Shogun main since you must be dual wielding for that bonus.

Warrior's Might is basically a chaser. Except it chases every attack without fail. Not that spectacular by itself but it's part of the basis of the broken group of the game. Second Sword + Swashbuckling (Buccaneer) has each swing trigger Warrior's Might (multi-hit skills are treated as "one attack" so only one chase) which can lead to a ridiculous amount of chases per turn. Plus, elemental forges (+10% base damage, essentially) work with Warrior's Might which leads to a lot of damage per hit. On top of that, Warrior's Might will never fail to chase unlike the Buccaneer chasers so every swing will generate a chase. All in all, things crumble before it.

As a sub, you're really only ever subbing them for Warrior's Might. The Katana skills aren't that attractive and 5-Ring Sword is only good with Second Sword changing it from 2-5 swings to 2-10 swings.
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Yggdroid - Honestly, the class is a cute idea but the execution of it is too much effort to be worth it. The bots aren't that great and they don't replace Antis/Prophecies well at all. The only (practical) damaging part of their skillset is HP Cannon which is this game's Revenge (damage done is based on HP missing) But it deals a pathetic amount of damage in a game where damage is king.

The Yggdroid also cannot be subclassed, which is fine I suppose since they don't have much worth subclassing for. Their main perk is their stat growth (good HP, STR, VIT) and their indefinite TP regeneration (though, they only have 60 TP). Basically, the Yggdroid makes for a really robust character with good STR ... that then uses the skills of their subclass. Their only damage passive is Overheat which hurts them as they attack and it isn't even that phenomenal of a boost to compensate for it (150% when maxed out but 127 damage taken per attack). They also lack any real damage boosting options (Berserker's Vow, Charge) unless they sub-Gladiator which ultimately means that the only class they can really sub at and be a competitive damage dealer is Gladiator (though, admittedly, they do make the best attacker with the Gladiator skillset).

Ultimately, the Yggdroid makes for a beefier attacking unit but without the damage of the other options except in one case. Their other primary role is as Yggdroid/Hoplite for a bulkier Hoplite but Hoplites are already bulky enough that it's basically unnecessary and you'd honestly rather have Hoplite/Utility-of-some-kind instead.