He's Frankenstein (the scientist) AND The Monster.

Stein is, in one word, insane.
In several words, he is... still pretty much insane. He's a scientist, curious by nature, and therefore everything in the world is his test subject. Most subjects include (but are not limited to): living people, animals, as well as himself. As such, he will do all he can in his power to learn more about them, right down to taking it apart and putting it back together (once again, this includes, but is not limited to: living people, animals, and himself.) While some people consider his obsession with dissection (and in most cases, vivisection) creepy or sadistic, he is actually revered as quite the genius. Spirit (his weapon and partner of long ago) mentions that while he feared Stein beyond all reason, he still held respect for the man, as he was the most powerful and most skilled of any meister to graduate from the DWMA.

Despite the obvious fact that he is completely unhinged, he's honestly just being silly! It's just usually at the expense of others. Some may consider his humor just as strange as his “hobbies,” but he’s actually a pretty lighthearted individual. His humor tends to run on the dry side, and most don’t catch it unless they know him. He often makes joke threats, and due to his blunt and slate-faced deliverance of said jokes, he’s usually taken quite seriously. If he’s intent on messing with someone, he will only carry it out to an extent; either the person being threatened gets terrified to the point of tears, or he breaks down in laughter. (That in itself gives him a sort of sick satisfaction, which only further leads people to believe he’s entirely insane, as well as sadistic… which isn’t necessarily the case. He’s actually pretty nice if he likes you. He just wasn't raised. Forgive him.)

Stein, while considered ”morally bankrupt” if you will, is not incapable of emotion. He holds a great deal of respect for Lord Death and his fellow meisters, as well as weapons he attended the Academy with. In certain situations, he’s even shown to present an almost paternal guardianship over his students. While his methods—and words—may seem a little brash, he has never once done anything with clear intent to harm—…injure—….kill(let’s go with kill) a student. He firmly believes all of his students are capable, skilled and powerful individuals, and wants nothing more than for them to succeed.

“ Thanks to his excellent powers of observation and his innate talent, Stein can control soul wavelengths extremely well. In this way, he can beat his soul wavelength against opponents or perceive foreign souls without a weapon. During a fight, he adapts his soul to the opponent. ”

Wavelength Control: Stein is described as having a flexible well as powerful soul wavelength with highly advanced levels of control over it, enabling him to use a variety of capabilities with only his wavelength. Stein displays rare and extreme mastery of his own wavelength thanks to his flexible soul and can match his wavelength with another's to nullify their wavelength attacks or wield Weapons that usually require great wavelength synchronization

Genius Meister: A very capable genius meister, Franken Stein's talent enables him to master most any weapon to a certain extent. He is considered to be more talented and skilled than even Maka's mother.

Scythe-Meister: Franken Stein is known to be an extremely skilled scythe-meister and normally employs Death Scythe as his main weapon of choice. He's very adept at handling a scythe, enough to spin and twirl a scythe weapon with ease.

Stein's Fighting Style: When using a scythe, his fighting style revolves around using his scythe weapon as a shield to block attacks and then immediately counter-attacking with his left hand with powerful attacks such as Soul Menace. His skill enabled him to fairly easily and quickly outmatch Crona using the Demon Sword against him. He was also able to fight on par with the witch, Medusa, and win albeit with a fair deal of luck.

Hand-to-Hand Combat: Stein is exceptionally skilled in hand-to-hand combat. With his unarmed combat skills combined with his other various skills, he's been able to easily take down Maka Albarn and Black☆Star when they both used their weapons in their first altercation and interaction with him. He seemingly gained the upper-hand in his spar with Black☆Star as well, even after the assassin improved his skills greatly. He's also not above abandoning the use of his weapon and relying on some of his unarmed ability, evident as he did so during his battle against Crona.

High Physical Abilities: Stein also possesses amazing physical prowess:

Enhanced Strength: Stein possesses enough strength to kick Crona a fair distance away when he saved Maka as well as break down the door of Santa Mario Novella Basilica with a kick, which Maka wasn't able to push open due to the doors only opening inwards. His punch also managed to send Black☆Star a far distance away.

Enhanced Speed: Stein possesses incredible speed, moving fast enough to appear as a blur as he rushed towards Medusa during his fight with her. He also managed to elude Ragnarok's eyesight moments after performing Experimental Ectoplasm when the weapon emerged from Crona's body.

Enhanced Endurance: Stein has great endurance for a human being, having taken multiple bloody-needles from Crona on the side of both his body and head and continuing to be able to fight despite the injuries. He's also survived being drilled through the stomach and hit by a barrage of Medusa Gorgon's Vector Arrows at close range.

Genius Intellect: Stein is an extremely intelligent individual, resourceful in the medical field from years of dissections and vivisections, and considered brilliant though eccentric. He performs surgery on Soul after his and Maka's first fight with Crona, though technically unlicensed as a doctor. There are various rumors surrounding him about tinkering with his own body and performing zombie experiments, eventually resurrecting Sid Barrett as a zombie. He's also knowledgeable in Soul Studies and even has knowledge on magic and spells.

Medical and Surgical Skills: According to Anya, Stein is a brilliant (but eccentric) unlicensed doctor. He's capable of performing advanced, life-saving surgeries as well as treating and aiding in ailments caused even by magic.