Anime/cartoon about two kids trying to depetrify all humans

Dr. Stone (2019) is the series you are looking for.

Beginning in April 5738 A.D., it's been over 3,700 years since a mysterious flash of light petrified nearly all human life. A 16-year-old genius named Senkū Ishigami is suddenly revived to find himself in a world where all traces of human civilization have been eroded by time. Senkū sets up a base-camp and begins to study the petrified humans in order to determine the cause of the event, as well as a cure.

Over the next 6 months, Senkū learns his revival was made possible with nitric acid. With this discovery, he develops a compound that will allow him to instantly revive others. He begins by reviving his friend Taiju Ōki, their classmate Yuzuriha Ogawa, and a famous martial artist named Tsukasa Shishiō, with the goal of rebuilding civilization with a focus on science.

Tsukasa ultimately reveals that he opposes Senkū's idea of forming a new scientific civilization, believing the old world was tainted and should not be restored. Instead, he desires to establish a new world order based on power and strength, going so far as to destroy any petrified adults he encounters in order to prevent them from interfering with his goals.

I found it by searching for anime "turned to stone" balloon, which brought me to the wiki entry for Volume 11 of the Manga.

IMAGINE WALKING TO A WORLD WHERE EVERY LAST HUMAN HAS BEEN MYSTERIOUSLY TURNED TO STONE...

The advent of the hot-air balloon means Senku and friends can start making accurate maps. And with more allies than ever, the Kingdoms of Science starts a doos revolution to create tasty, long-lasting bread to feed everyone in the kingdom. Then, while testing their new motorboat in nearby waters, they intercept a cryptic message. Could there be others who survived the petrification?!

Trailer

It might be the 2002 Korean anime Chaechaepong Kimchipong, as in these earlier questions:

• Animated series whose main character wears a red gauntlet on his arm
• Old cartoon where villain turns villagers into statues (disclaimer: I answered it)
• Anime/cartoon where a kid has to save his grandma that turned to stone (disclaimer: I also answered this one)

This anime seems to be one of a kind in terms of stuff almost entirely lost. No episode can be found on the Internet to confirm how much it matches, several people search it with no success (here on 9GAG), someone even claims the original Korean dub is lost (link).

Proving that this may or may not be the anime at stake is then based mostly on the recollection of former askers (see links at the beginning of the post), and bits from the opening:

• Magical girl, check. Her hair is pink, I don't know if her look is what you'd remember as "something odd with her hair".
• I tried various translation services on this wiki page (in Korean), and all state that Tochi avoided becoming a stone because something something large stone tower. Literally what I get from Google Translate is "Torch, who accidentally acquired Kimchi Stahl in a large stone tower, escaped from becoming a stone alone without knowing the English."(?), and Systran gives me "In a large stone tower, Tochi, who accidentally holds Kimchi Stahl in his hand, is free from being a stone, without knowing English." (??)
  Point being, that stone tower may be a well, or the recollection of a well might be a mistaken memory of a stone tower.
• This (0'22 in the opening) vaguely makes me think of a fruit-sized glass "sphere".
• There were bits with food being taken out of a device to summon creature powers in the earlier questions.
• So was it being broadcast on MBC3, and the main character having a yo-yo (your "telescopic handle tool" maybe? Or the device unfolding at 0'46 in the opening?).

What would not match is the "mad scientist"; if I am to believe the summary above, and this one, the villain is the evil Lord Aegross (curses, not science). I'm also not sure whether the girl's mic-looking device (wand?) can shoot like a cannon.

In the most peaceful village on Earth, Singleland, a boy named Tochi lives a normal life with his grandmother. One day, all the creatures that lived in their land are suddenly petrified, leaving Tochi as the lone survivor.

Bewildered and frightened, Tochi meets a travelling little witch named Milo who informs him that what happened to his village, and many other villages including her own was due to the curse of the Black Mage Army. She reveals that he wasn't petrified because he had the magical Kimchi Stalks, therefore she gives him the "Chae Chong", a summoning tool, which only the person with Kimchi Stal can own. The "Chae Chong" can summon a Kimchi Pong when you put a Kimchi Stall, a powerful magical creature, which they use to fight the Black Army.