Thanos and Scarlet Witch have come across each other on several occasions, none of them being great memories for the latter. Disregarding the MCU power networks, however, and only taking into account their innate Marvel abilities place both these characters on a more-or-less equal footing.
Both of them have access to their full strengths, except for the Infinity Gauntlet, which would just be cheating on Thanos’ part. In fact, even with the Stones, the conclusion is incalculable (given Scarlet Witch’s show of power in Avengers: infinity War.)
Magic Versatility: Scarlet Witch
Thanos doesn’t really need magic, or so he thinks! In fact, aside from cursing Deadpool with immortality, he only uses what little magic he knows to create marvels of engineering (like his so-called throne.)
Wanda has a wide range of magical capabilities, armed via her hex bolts — she can burn, atomize, explode, manifest, enhance, or negate almost anything. Initially, her spell-casting was spontaneous, and usually ended up causing horrific outcomes, but she has since developed a far greater command over her hexes.
Thanos is beyond smart, making geniuses like Reed Richards, Tony Stark, and Beast look like idiot children in comparison. He has been able to manipulate some of the most cunning minds in existence (like Loki.) for his own purposes.
Thanos’s intelligence in battle is extremely high, for instance, when he defeats the Champion of the Universe by simply teleporting away from his final attack. The resulting impact destroys the planet, stranding the Champion in outer space (from which Thanos offers him refuge in exchange for the Soul Gem.)
Allies: Scarlet Witch
If it wasn’t obvious from the movies, Scarlet Witch has comrades who are more than capable of handling an Infinity Gauntlet-wearing Thanos (except for Starlord.)
Captain Marvel, for instance, shows that she is far stronger than him when she pins him in place, only getting knocked away by Thanos clever use of the Power Gem. In fact, the Avengers, the X-Men, and the Fantastic Four together would have had practically zero trouble in taking him down.
Wanda’s abilities do not require her to be physically strong, or even athletic. In physical combat, Thanos is on an entirely different level (to pretty much everyone.)
A testament to his durability is shown when he only gets annoyed after receiving Black Bolt’s electron screams head-on, knocking out his opponent in anger. He manipulates cosmic energy within his body, using it to heal from severe injuries or maintain an aura of immunity to all biological illnesses.
Long Range Attacks: Scarlet Witch
Although Thanos is invulnerable, he doesn’t have the potential to carry out significant damage from a (great) distance. In other words, the winner of the Long Range category is Scarlet Witch.
To be clear, she doesn’t need to be in the same room, building, city, planet, universe, or even dimension in which her hexes take effect. One of the best known examples of this ability is when Wanda switches off the mutant gene, devolving every single one in the entire multiverse.
Scarlet Witch is in her mid-twenties, assumed from her appearance. Thanos, on the other hand, is at least a millennium old and has been plotting his various schemes for pretty much the entire time.
He has managed to gather and control innumerable armies, all of whom he somehow manages to brainwash into mindless drones. Thanos is clearly capable enough to force the extremely powerful members of what later becomes Black Order into indentured servitude.
Reality Warping: Scarlet Witch
Scarlet Witch can mold (or shatter) both time and reality according to her whims. She exhibits a degree of omnipotence — in the fact that she has been able to bring certain dead heroes back to life, such as Simon Williams, Clinton Barton, and her brother, Pietro Maximoff.
Her authority is often paramount, given that she can counter the extra-cosmic forces of The Beyonders, although she was only able to prove the possibility while fighting Meggan.
Defensive Abilities: Thanos
Possessing almost flawless levels of physical sturdiness, Thanos is undefeatable in most fights. On top of everything else, he is extremely agile and possesses an incredible set of reflexes, both of which come in handy in battles against tough adversaries.
One of his main defenses is cerebral; that is, he has constructed a psionic shield within his mind to protect it against psychic probes. Thanos can also float around in the harsh vacuum of space, or deep inside volcanoes and oceans, by generating a force-field around his techno-mystical chair.
Nexus Being: Scarlet Witch
Scarlet Witch contains the core of the universe within herself, making her a living metaphor for everything that exists in 616. As a Nexus Being, she is of utmost importance in maintaining universal equilibrium, basically acting as a keystone.
In Avengers: Forever, the super-villain Immortus wants to kill Wanda, simply because her future children might be powerful enough to “rock the Cosmos itself.” It takes a lot of effort to destroy a force like Scarlet Witch, and succeeding might mean the end of all things.
Winner: Scarlet Witch
Irrespective of Thanos’ might, or even his rather high success rate, there is little to no chance he would survive a fight against Scarlet Witch. She possesses the power to edit the history of the universe, which she also uses (accidentally) changing the probability spans of all events that are yet to occur.