Warning: Spoilers are scattered liberally throughout this entire application.
Fears: At this point in the timeline, Emil’s world has been turned upside-down in a crazy loop because he isn’t looking to wake up Ratatosk anymore. He is Ratatosk, and with this memory comes a whole new can of worms in that Ratatosk had been planning to kill off all of mankind in revenge for the destruction of his tree and had started by murdering a researcher who happened to tick him off. The visions of Richter trying to kill him were true, because after Aster’s death Richter had indeed injured Ratatosk badly enough to reduce him to a core.
That said, Emil’s quite reasonably worried he’ll try to annihilate mankind again. He had the intentions, the means, and the motivation. His other self isn’t the nicest guy, and even when he was reawakened Ratatosk managed to show just how much he valued others by placing a fake core on the girl who’d awakened him to lure enemies away from himself-the same girl who’d fallen in love with Emil (and whom Emil had some feelings for as well). Emil doesn’t want to kill people, but if he ever returns to being the same angry summon spirit who killed Aster he won’t have any of those inhibitions and he’s afraid of that. Simply put, he doesn’t want to hurt others (though he’s fully aware that he’s injured people in battle to protect himself and those he cares about) or see his friends get hurt.
Emil also has a long fear of his aunt and uncle. Maybe it’s because of their treatment of Emil before he became a Knight of Ratatosk, or just the way all Luin hated him. Maybe it’s because they’re a subconscious reminder of a time where Emil was hopelessly weak. Either way, upon encountering his uncle again in a sidequest Emil lost the confidence he’d been slowly building up and was reduced to the same stuttering boy he’d been at the start of the game, even physically hiding behind someone. If the rest of the game is any indication Emil’s since grown to hope for a real relationship with them rather than an awkward mutual fear, but he’s also very nervous about trying to approach them.
In general, Emil’s not a huge fan of conflict, though he’s also grown to understand the importance of facing what makes him afraid. Emil knows he was a weak person before he began his journey, and he still has his moments of weakness and doubt-as late as the end of the sixth chapter he’s still making remarks in his journal like "Me, I’m just pathetic. I may have borrowed Ratatosk’s power, but outside of that I’m just a useless kid." He’s never going to be a really aggressive person, though he has become more assertive since he started out.
What Ratatosk’s personality fears is harder to pin down specifically. The most obvious one is that which will hurt him a lot, like a huge ball of mana larger than a grown man coming right at his face. Others involve his friends getting hurt (though he’s a lot more closemouthed about it) and in general, not being strong enough. He disapproves of Emil’s kindness because he believes it’s weak, and that won’t accomplish anything in the end. One of the best examples of this was when he believed Richter had killed Marta and he blamed it on Emil: "If I was more powerful, I could’ve stopped this! If I was always me, I never would’ve let this happen!" Even later on, when he decides to stop taking control outside of battle after he does a nice thing to help Marta, Ratatosk never quite trusts Emil to be strong enough to protect her.
Weaknesses: As mentioned above, Emil’s suffered a huge blow to his sense of identity. For a while Emil thought he was the researcher Aster, nearly killed by Richter and turned amnesiac, and he’d come to terms with that-but as it turns out Emil himself killed Aster as Ratatosk, the very one he had been trying to help awaken for the entirety of their journey. He isn’t chasing after an object other people also happen to be chasing chasing anymore, he is the object, and with this knowledge comes the fact that Emil Castagnier as he knows himself is not real and all his memories of childhood are fake.
Identity confusion? Oh, yes. The first thing he says to Marta after that is "Who am I?" and he continues to doubt himself despite her support, even when others trust him to fix things. Though everybody he’s met since waking up after the battle with Richter believes he’s Ratatosk, Emil still has trouble coming to terms with it himself because it contradicts sixteen years’ worth of memory as Emil Castagnier (something he’s struggled with previously when thinking he could be Aster, only now freshly upturned) and as he says later: "Well, I want to be human." Being just Emil Castagnier, Knight of Ratatosk would be easy compared to suddenly being a fake personality of the ancient spirit he’d been trying to awaken, but all the evidence points the other way and he’s not stupid enough to deny it.
Aside from that, Emil is timid by nature and tends to yield to others in times of doubt or fear. Occasionally he’ll be too trusting; the night before he’s taken, he trusts an enemy Vanguard member who comes to him and Marta for help and it ends up getting Marta abducted and Emil trapped in a room with a literally insane Vanguard member. He’s gotten much braver than he used to be and is learning to stop running away from his problems and accept what he has to do to solve it, though sometimes he won’t-he usually needs a real incentive and/or a push from friends.
Ratatosk, on the other hand, can be quick to anger and sometimes too stubborn to learn his lesson. His ruthlessness tends to turn people off from him and he can be narrow-minded in his goals.
Both sides tend to bottle personal problems up without a word to anyone, which can sometimes end with dramatic results, i.e., Emil accumulating guilt over killing people/sealing them away until he nearly gets his friends to kill him or Ratatosk not saying anything about how Emil gets all the acknowledgment from his friends until he explodes at Marta.
Strengths/Abilities: Emil is a strong fighter, thanks to his experience from collecting the Centurions’ cores in addition to Ratatosk’s natural power. In battle, a few of his attacks have elemental attributes such as fire or darkness thanks to the Centurions-as Emil awakens each Centurion, he gains the ability to use their attribute in battle.
Ratatosk being the lord of monsters, Emil also has a general connection to monsters as well as the ability to make pacts with them after fighting them in battle, which enables him to use monsters as battle companions (though all this is officially not applicable to monsters in Dollsyhouse). Monsters with him include Mattias the Ravenous, a small spellcaster; Ixia the Lailah, a plantlike creature; and to not crowd stuff up (and because a fairly standard party usually includes two monsters) I’ll stick with those two.
Ratatosk can also use Ain Soph Aur, a powerful arte that involves charging mana on his sword and then swinging the sword to throw the gathered energy at an enemy. Since Ratatosk serves many purposes in his world he has other powers, but the others shown in canon are both not applicable in the Dollsyhouse setting and way too powerful to normally be allowed otherwise (e.g., warping dimensions only to transport Centurions, though others can also get caught in this if they’re unlucky, and when restored to full power later on Ratatosk was able to rewrite the laws of natural mana flow).
Emil’s also a very good cook. The "normal" Emil tends to make his dishes into art by carving apples into rabbits, sculpting turtles out of pumpkin, and so on, but when Ratatosk does the cooking his food looks like an inedible mess yet still tastes just as good.