The unique skillsets of Clone Force 99 mean that each member is also uniquely intelligent. A character like Tech has book smarts and analytical thinking, along with a strong mechanical aptitude, linguistic skills, and an in-depth understanding of technology. Other members like Echo demonstrate their smarts through adaptation and questioning the morality of certain decisions.
Beyond Clone Force 99, there are many other clever characters in The Bad Batch. Characters like Cid and Fennec Shand use their smarts to make money in the early days of the Empire while a character like Vice Admiral Rampart uses his wit in a very public sense. Each character in the series demonstrates a different kind of intelligence while navigating a rapidly changing galaxy.
Wrecker
Wrecker has a more limited vocabulary than his peers. This sometimes prevents him from understanding certain subjects and what people are saying to him, such as when Jedi Master Depa Billaba told him that the Bad Batch's exploits were impressive or practically any time Tech explains something technical. In addition to his vocabulary, Wrecker sometimes rushes into situations without thinking about the logical and often dangerous consequences that will follow.
It would be a mistake to believe that Wrecker is unintelligent, though. A great example of his type of smarts is when he teaches Omega how to disarm a thermal explosive by showing her how to do it. He's also wise enough to have her practice with a harmless smoke bomb instead of with live explosives. This example alone demonstrates mechanical aptitude, communication skills, and common sense that are all part of Wrecker's intelligence.
Crosshair
Without knowing how much of Crosshair's thinking is his own and how much is the Order 66 inhibitor chip, it is difficult to fully assess Crosshair's intelligence. His insistence on blindly following orders and not questioning them is arguably a sign that he is less intelligent than the rest of the Bad Batch and has weaker independent thinking skills.
Even when he follows orders, though, Crosshair demonstrates a certain savvy. He saw through Hunter's lies about watching Caleb Dume falling to his death and could tell that Hunter let the Jedi Padawan escape. When an Imperial soldier questioned his authority on Onderon, Crosshair knew the smartest move was to kill the soldier.
Cid
Cid knows how to gather intelligence and how to profit from the information she possesses. This made her a valuable informant for the Jedi Order during the Clone Wars and has helped her continue to profit in the early days of the Empire. She has figured out to transition between these periods better than most and has so far been able to conceal her connections to the Jedi.
She is also able to recognize when someone has a valuable skill and how to use those skills to her advantage. After the Bad Batch successfully brought the rancor Muchi back to her, she saw them as valuable assets and hired them for many future jobs. She also recognized Omega's talent when playing dejarik and figured out how to profit from that as well.
Rampart
Through cleverly convincing people to act against their own self-interests, Vice Admiral Rampart has been integral to many of the Empire's early initiatives. Rampart convinced people all over the galaxy to get chain codes. He made it sound like a great deal, as chain codes would allow citizens to convert their Republic credits into Imperial credits and would allow them to easily book passage off-world. This prevented most people from realizing that the chain codes were really about the Empire registering everyone, tracking them, and controlling their movements through the galaxy.
Rampart pulled off more deceitful maneuvers on Ryloth. He made it seem like a Doonium mining facility was in the best interest of Ryloth's economy and prosperity, even though it was really about enabling the Empire to control a resource needed for the construction of the Death Star. He also made it seem like he valued Senator Orn Free Taa's loyalty to the Empire, yet Rampart ensured that Taa was shot in an effort to frame Cham Syndulla and further assert Imperial authority on Ryloth.
Fennec Shand
Fennec Shand successfully hunted down Omega on multiple occasions and kept her away from Lama Su. Instead of simply kidnapping Omega on Pantora, Fennec formed a connection with Omega, appearing to help her out and offer her valuable advice.
Even though Omega ultimately evaded her on Pantora, Fennec used Nala Se's intel to arrive on Bora Vio before Cad Bane. This gave Fennec the opportunity to kill Cad Bane's contact and take the credits owed to him, which gave her an advantage over Cad Bane before he got to Bora Vio. She outsmarted the seasoned bounty hunter in combat and sabotaged his ship so he wouldn't be able to pursue her or Omega.
Hunter
Despite many difficult circumstances, Hunter has been able to make many good choices as the leader of Clone Force 99. He made the call to return to Kamino to save Omega. While that choice wasn't practical, it was the right thing to do. After escaping Kamino, he decided to go to Saleucami as he knew Cut Lawquane was an ally and the perfect person to help the Bad Batch begin navigating their post-Clone War lives.
While Hunter usually strives to complete the jobs Cid gives to the Bad Batch, Hunter has been able to recognize that there are sometimes more important elements in play. For example, he let the Martez sisters hold onto the tactical droid intel, as he wanted the information to be in the hands of people fighting the Empire instead of whomever Cid would sell the intel to.
Nala Se
Nala Se has managed to stay in a position of power on Kamino while surreptitiously undermining the Kaminoan Prime Minister Lama Su. Nala Se secretly helped Omega and the Bad Batch escape Kamino, even though Lama Su wanted to experiment on Omega and use her genetic material.
Shortly after helping Omega escape, Nala Se hired Fennec Shand to track down Omega and prevent her from falling into Lama Su's hands. She told Fennec that Taun We would be meeting Cad Bane on Bora Vio, which gave Fennec the upper hand before Cad Bane arrived with Omega.
Omega
Omega knows how to use her wits and available resources to make the best of difficult situations. One of the earliest examples of this is when she figured out how to track the Ordo Moon Dragon and get the necessary ship components back from it when Hunter was unconscious and she was alone.
Omega also has a strategic mind. Her strengths are well-known on Ord Mantell where she used strategy to best numerous opponents at dejarik. Another sign of Omega's intelligence is that she is curious and is constantly asking questions to better understand the galaxy around her. The things that Omega does not understand are usually due to her lack of life experience outside of Kamino and not due to a lack of intelligence.
Echo
Echo was always an intelligent soldier, but he truly showed his intelligence when he adapted after being brutally tortured and experimented on by Wat Tambor and the Separatists. Using his creative thinking and his cybernetic modifications, Echo was the key to turning the tide during the Battle of Anaxes.
As a member of the Bad Batch, he has used his intelligence to hack into heavily guarded systems. Most importantly, Echo always thinks for himself and doesn't just go along with what the rest of the Bad Batch is doing. He frequently questions the choices they are making, whether those choices are in their best interests, and whether the choices are moral.
Tech
As the brains of Clone Force 99, Tech is unsurprisingly the smartest character. He has an endless store of trivia and facts in his head, ranging from life-saving and practical information to knowledge that is absurdly obscure and trivial.
In addition to his knowledge, Tech's analytical mind and his ability to use the tools he has allows him to effectively analyze any new data or information that he receives. Whether it's forging chain codes, fixing a ship, or communicating through an uncommon language, Tech can tackle almost any task.