I faintly remember an anime I loved but didn't finish.
There are a boy and 2 girls in a cafe in one episode. They use crystals to see what magical powers the boy has. They are elemental crystals and one crystal showed if you had a unique power. The boy has a few elemental powers, which was rare, and he had an original one too.
A young, easy-going guy died in a tragic accident, and God felt bad, so reincarnated him in a fantasy world after cranking his attributes up to 11 and letting him take his smartphone.
It's a harem anime, borderline-ecchi, where the protagonist goes on adventures and befriends various young women, solving problems through clever applications of the large number of spells that he learns enhanced through the common functionality of a modern smartphone (maps, searching, photos, etc.)
His first contacts in the new world are two sisters who, while being capable warrior/mage, he rescues, and they introduce him to the system of magic using crystals that contain/enable spells of different affinities.
I think what you're looking for might be Full Time Magister, I’m not entirely sure though.
From MyAnimeList.net:
The aloof high schooler Mo Fan has found himself in a universe similar yet distinctly different from his own mundane one; it's a place where magic has replaced the essence of science. Here, the most capable students are taught to master the wonders of spellworking to fend off large devastating beasts that lurk in the forests surrounding the city.
Like his previous life, Mo Fan remains the son of a poor laborer and the older step-brother to a crippled sister. Despite these disadvantages, he dreams of attending a magic school to become a magician—a highly respected and lucrative trade—in order to repay his father for his hard work.
Mo Fan is accepted into a renowned magic institution. However, rumors spread about his poverty and lack of magical ability, labeling him as the laughing stock of the school. Nonetheless, Mo Fan manages to harness not only the powerful fire element, but also the rare lightning element! Now armed with dual abilities, what dangerous encounters will the versatile mage face?
The protagonist matches the description of having elemental powers, including one very rare ability.
Is it Steven Universe?
Steven Universe is an American animated television series created by Rebecca Sugar for Cartoon Network. It premiered on May 21, 2013 with its pilot, then on November 4, 2013 with its first season. It is Cartoon Network's first animated show created solely by a woman. It is the coming-of-age story of a young boy, Steven Universe (voiced by Zach Callison), who lives with the Crystal Gems—magical, humanoid aliens named Garnet (Estelle), Amethyst (Michaela Dietz), and Pearl (Deedee Magno Hall)—in the fictional town of Beach City. Steven, who is half-Gem, has adventures with his friends and helps the Gems protect the world from their own kind. The themes of the series include love, family, and the importance of healthy interpersonal relationships. Books, comics and video games based on the series have been released, and a television film is in development.
The series has developed a broad fan base and has been critically acclaimed for its design, music, voice acting, characterization, prominence of LGBTQ themes and science fantasy worldbuilding. The series won its first GLAAD Media Award for Outstanding Kids & Family Program in 2019, becoming the first animated series to win the award. It also received its first Peabody Award for Children's & Youth Programming in 2019. It has been nominated for four Emmy Awards and five Annie Awards. Its fifth season concluded in January 2019.
Steven Universe is set in the fictional town of Beach City, Delmarva.[4] The Crystal Gems live in an ancient beachside temple and protect humanity from monsters and other threats. The Gems are ageless alien warriors who project female humanoid forms from magical gemstones at the core of their being. The Crystal Gems comprise Garnet, Amethyst, Pearl and Steven—a young, half-human, half-Gem boy who inherited his gemstone from his mother, the Crystal Gems' former leader Rose Quartz. As Steven tries to understand his gradually expanding range of powers, he spends his days with his father Greg, his friend Connie, his magical pet lion, other residents of Beach City, and the Gems. He explores the abilities inherited from his mother, which include fusion—the ability of Gems to merge their bodies and abilities to form new, more powerful personalities.
The series's first season gradually reveals that the Crystal Gems are remnants of a great interstellar empire. During their missions they visit ruins that were once important to Gem culture but have been derelict for millennia. The Gems are cut off from the Gem homeworld, and Steven learns that many of the monsters and artifacts they encounter are Gems who were corrupted by a Gem weapon of mass destruction and can no longer maintain rational, humanoid form. By the end of the first season, Steven learns that, millennia ago, the Gem empire intended to sterilize the Earth to incubate new Gems, but Rose Quartz led her supporters, the Crystal Gems, in a violent and apparently successful rebellion against this genocidal plan. In the present, the Gem empire's machinations again begin to extend towards Earth with the arrival of hostile envoys Peridot and Jasper.
In the second season, Peridot allies with and eventually joins the Crystal Gems to prevent Earth's destruction by a Gem "geo-weapon" buried in the planet. During the third season, Lapis Lazuli, an errant Gem from Homeworld, decides to live on Earth with Peridot; Jasper is defeated and captured, and Steven learns that his mother shattered one of the Gem empire's matriarchs, Pink Diamond. In the fourth season, as Steven wrestles with his conflicted feelings about his mother's actions, the Gem empire leaders Blue Diamond and Yellow Diamond return their full attention to Earth. In the fifth season, Steven learns that in fact his mother was Pink Diamond, who faked her death to assume the identity of Rose Quartz; he uses this revelation to try to persuade the other Diamonds to take responsibility for and fix the damage they have caused.
