General Skill/Experience
Marisa has been fighting and exterminating youkai for decades at this point (nearly 30 games across over 25 years, including numerous manga and light novels), to the point where she's learned the smell of blood from experience on the battlefield alone. To her, a world without conflict is Hell, and she claims to be an experienced veteran. She regularly engages in image training (essentially playing out an entire battle in her head using mental images), winning 101 times out of 100. Not as impressively,
she can also dodge near-point blank gunshots from characters comparable in speed. She's highly skilled in the art of danmaku, creating highly complex bullet hell patterns on the fly, and dodging whatever everyone else throws at her. Aside from that, she's an expert in improvised weaponry, using a regular broomstick as an improvised rifle, or stringing together melee combos while simultaneously using it for flight. During
Unconnected Marketeers, she was able to master the use of ability cards so quickly that their creator
outright mentioned her brilliance in using them. She possesses
encyclopedic knowledge on hundreds of different of techniques, many of which she's only seen a single time (
this sort of insane memory is consistent btw), detailing countless specific traits of these spell cards in the process. She's also highly skilled in copying magic, being able to do so after seeing a technique once, and magicians have a tendency to experiment with such techniques to improve it beyond what its original user can do (on top of mimicry like this being implied to be the norm).
Alongside Reimu, she can track down dangerous youkai across all of Gensokyo for days straight without any rest, or climb entire mountains that are being constantly battered by high winds without any equipment. During the events of LoLK, her canon ending involves
getting a no-miss 1CC throughout the entire game (which basically just means doing a single flawless run in what is considered one of the most difficult Touhou games).
Her skill is so great that she has become one of the strongest known users of fire magic in Gensokyo in a short timeframe, despite her natural water affinity (something already noted to be "quite a feat"); This is specifically important because using magic that doesn't align with your elemental affinity can
straight up nullify the spell you're using, which means Marisa has trained to overcome supernatural power null just by being
that good at magic. Semi-relatedly, but she's a savant in the field of magic, pushing forth new theories of magic and tackling pre-existing theories, such as elemental affinities being limited to five types, and the new spells she develops surprise even youkai. Her knowledge in magical theory is great enough that centuries old youkai like Suika
admit her theories are spot-on; This includes breaking down the hidden power of the oni, which is inherently impossible to even fathom, as it is powered directly by remaining unknowable.
Getting a little more extreme,
she can dodge weather like rain or snow, and in fact considers them
easy to dodge. This is supported by how even fodder enemies like fairies train by dodging falling snowflakes, which if you didn't know,
is physically impossible. She's also highly adaptable, going from being dumbfounded by the illusion obscuring the true moon in
Imperishable Night, before later seeing through it in her bad ending (the game takes place over the course of about 5-6 hours lol). In IaMP, she's noted to have terrible martial arts skills, but within the course of a couple of fights, she's mastered CQC to the extent of matching and later even surpassing Meiling, a highly skilled martial artist who trains regularly and whose skills are a rarity among youkai.
Enhanced Senses/ESP
Marisa has a lot of these so I'll just list them all lol
She can sense
spatial distortions, sources of magical energy,
a person's aura, the
pure energy possessed by Junko, someone's power level, or the amount of "spring" they possess. She's noted to have a good nose that lets her detect the smell of blood or youkai, the smell of death itself, treasure, or
track down the Occult Balls across Gensokyo in a single day, something noted to be a ridiculous feat. This includes locations that are above the clouds, or even The Palace of Earth Spirits, a place within Former Hell, which is an Otherworld and therefore a completely separate dimension that
can't be accessed normally. Her eyes and nose are so sensitive that it's actually extremely easy for her senses to overwhelm her. She can see through the disguise of experienced tanuki like Mamizou, something
not even Reimu can do (see below). She's also fought in dark conditions totally fine, even when afflicted with Mystia's ability to induce night blindness. Her ESP can detect the magic power being manipulated by Okina Matara, something that jizo like Narumi are unable to do despite their innate ability to detect magic power. For some ungodly reason, her ESP also lets her detect if a player has continued.
Stealth
For starters, she's able to
sneak into heavily guarded locations like Eientei, which was being guarded by a number of youkai rabbits. Youkai rabbits possess the already heightened senses of regular youkai (vision in pitch-black conditions, infrared vision, etc), on top of
even sharper senses, which also includes the ability to see the souls of living beings, or possibly even the "pulse" of the moon. Not only that, but they can
detect people's wavelengths,
tap into the minds of those around them, and are inherently linked like a pseudo-hivemind. Marisa snuck past
dozens of youkai rabbits with minimal effort.
This is somehow not her most absurd feat; While speaking with Reimu on one occasion, they were interrupted by Yuyuko and Satori. When Reimu mentions Marisa,
she realizes she's just... gone. So despite being in two people's direct line of sight (and a third person's peripheral vision), Marisa practically just vanished into thin air. Already absurd, but let's look at the enhanced senses she'd have to bypass to do that:
-Reimu
has an inherent intuition that lets her track down people and locations innately,
quite literally a 6th sense. It is superior to other forms of ESP, and she's used it to
track down locations like Eientei, which exists outside of
time, history, and the world itself. She can
pinpoint the locations of 18 separate beings at once just by focusing, easily see through
illusions or
disguises,
detect people's auras,
see nonexistent beings, follow trails of power to track people down, or
detect the energy leaking from a person's body. Perhaps most notably though, is the aforementioned feat of navigating her way to Eientei. This is something characters like Aya cannot accomplish deliberately, and
her senses are good enough to hear the sound generated by entire alternate dimensions (cosmic awareness lmao), be described as completely transcending the world that Marisa perceives, feel energy that is on the verge of disappearing from existence,
hear rumors on the wind, or just...
generally be really good. So, Marisa's stealth > Reimu's senses > Aya's enhanced senses bordering on cosmic fvcking awareness.
-Satori has some of those good youkai senses I mentioned before, in addition to her abilities as a telepath; Even when she doesn't intend to, she's constantly reading not just the thoughts of those around her, but
the leftover traces of those thoughts that remain after a person has already disappeared... Which means Marisa's stealth isn't just evading physical detection, but also completely eliminating any traces of her own thoughts.
-Yuyuko admittedly doesn't have much in the way of bullshit feats, but she can
detect a corpse under a tree from meters away and immediately deduce how long it had been decaying for.
She's also
disappeared from the perception of Flandre, who can detect a person's disposition. So, in conclusion, her stealth borders on straight up invisibility.
Social Influencing
Idk if this really counts as skill, but eh, fvck it. She managed to trick Tewi Inaba into eating a poisonous leaf, and Tewi is someone whose knowledge on poison is superior to that of Medicine Melancholy, someone who is quite literally made of poison, was born as a result of poison, and has mastered the use of various poisons to a degree that nobody else has. She could talk Yorihime out of killing her and a handful of others despite being tied up, or make Utsuho, someone consumed by divine madness driving her to reduce the planet to ashes, completely submissive to her.
Intstinctive Reaction
Marisa has perhaps some of the most insane showings of this I've seen before. On two separate occasions, she dueled and won against Koishi Komeiji, who
does not exist. The nature of her nonexistence makes her impossible to perceive (something Marisa herself notes), as is her danmaku. All traces of her existence are erased, and even in the case someone does detect her, her attacks are completely unreadable and they forget about her in a matter of seconds. Notably, due to lacking a conscious mind,
every single action Koishi takes is subconscious, meaning she has 24/7 instinctive action. This is on top of her manipulation of the subconscious, wherein she is able to make people completely unaware of her attacks, basically perceiving them as if there's no threat at all.
There is, of course, also the time she
casually dodged attacks from Youmu Konpaku while sitting down and drinking (and her sake not even drop!). Youmu is a master swordswoman in her own right, but in this scenario she was also being actively amplified by Clownpiece's torch, which brings out a person's full potential. Even without that, though, she's fast enough to casually blitz Aya Shameimaru, as well as fight entire danmaku battles and win without realizing it. Aya herself can also fight entire battles without realizing, and is so fast that Sakuya needs to use her time stop to track her movement... and
Sakuya is able to keep up with beings who can move faster than Marisa can track (so Youmu's combat speed >>> Aya >>> Sakuya >>> Marisa). To recap, that's three degrees of blitzing and instinctive action being dodged by someone who's casually sitting down, enjoying a nice meal, and chatting with her friends.
FWIW, she can also dodge attacks she can't perceive using her mind's eye, but that just supports what I've already said.
Scaling
Given the nature of Touhou, there are a lot of skill feats other characters have performed, and Marisa scales to a good number of them. Compared to youkai, it appears as though her dodging is like that of bits of paper floating through the air; Impressive, given youkai have the precision to roll dice in such a way that perfectly replicates the previous roll's angle, force, rotation, and result. Her danmaku is on the same level as gods like Suwako, who has lived for hundreds of years and was a noted leader in her own time. She's fought against and defeated enemies like Yuyuko, who can fight with her eyes closed, or Remilia, who is stated to be a spell card veteran and can fight her own afterimages. She's superior to fodder enemies like moon rabbits, many of whom are war veterans, and can learn how to engage in spell card duels and even beat three separate, more experienced opponents mere seconds after their first exposure to the concept.
TL;DR: Marisa sweeps Sora in skill and it isn't even close.