The Suicide Squad is of course DC's long-standing team of villains carrying out U.S. government missions under threat of death. Marvel's Thunderbolts are the reformed Masters of Evil, assembled as a heroic team by a freaking Nazi in an effort to conquer the world. The two teams represent different sides of a disfigured coin. They're different visions of what it looks like when supervillains are forced by circumstances to do heroic things.
Which team is more powerful? Both the Suicide Squad and T-Bolts bring unique assets and liabilities to the field. In the battle between the cynical, the predatory, the innocent, and the conniving which emerges as the winner? It depends a lot on which version of each team you look at. That said, considering their contemporary line-ups, we can look at attributes like...
9 Size: Suicide Squad
The most prominent current version of the Suicide Squad is the one discussed for the upcoming sequel to the 2016 film. It includes Ratcatcher, King Shark, The Polka-Dot Man, Peacemaker, Harley Quinn, Deadshot, and Rick Flag. It's hard to imagine The Squad without Captain Boomerang, so he can count as a bonus member. 8 members total, not counting Amanda Waller.
The current Thunderbolts team is back under (Nazi) Baron Zemo's control, making them one of the most unapologetically unreformed versions of the team. Zemo leads them in the guise of Citizen V. He's followed by Ghost, Moonstone, Fixer, Jigsaw (the Punisher villain, not John Kramer), and the Radioactive Man. It's their smallest roster to date, putting them at a disadvantage against the Squad.
8 Overall Power: Thunderbolts
This is also one of the weaker versions of the Thunderbolts, which has boasted members like the Juggernaut and Marvel's Superman clone, Hyperion. That said, Suicide Squad tends toward low-powered but super-skillful operatives who lack a lot of raw force. The current lineup is no exception. Only Ratcatcher and King Shark have superhuman powers, and Rat's Willard-esque abilities aren't the most impressive.
Even this low-powered, more Suicide Squad-ish T-Bolts team has two powerhouses on it. Moonstone who, in addition to her selfish genius, possesses powers similar to The Vision, and the Radioactive Man. Despite his dopey name, the Radioactive Man has fought Thor to a standstill in the past. Fixer is also a nearly unkillable mechanokinetic, and Ghost is a long-standing Iron-Man threat, tilting the scales further towards the Thunderbolts.
7 Strongest Member: Thunderbolts
As mentioned above, both Radioactive Man and Moonstone have frightening powers. Moonstone has more flexibility, but in terms of raw force, the Radioactive Man's force fields, strength, and radiation blasts make him the strongest player on either roster.
The Suicide Squad's strongest player is undoubtedly King Shark. He's a demigod, and his colossal strength and indestructible body should never be underestimated. Even so, KS would struggle in a straight fight with either Moonstone or Radioactive Man. He could win either fight, but with their power and intelligence each would have a considerable advantage.
6 Teamwork: Thunderbolts
Both of these teams struggle with teamwork but the Thunderbolts have never actually eaten each other on a mission (thanks King Shark). The Suicide Squad has such a long history of dysfunction and murderous backstabbing that, despite moments of impressive cooperation, they never feel like a team. The only members of the Squad that don't understand that the others will sacrifice them are the dead ones.
The Thunderbolts may not always work together as a team, but they form effective units within the larger organization. Songbird isn't on the current roster, but her friendly alliance with Radioactive Man is a good example. The team has also usually coordinated well under a leader's guidance. While it was a different team, this feature has let them take down colossally overpowered opponents like Graviton.
5 Leadership: Suicide Squad
Baron Zemo is a brilliant mad scientist and strategist, but his arrogance and lack of compassion limit him. He's cold and cruel to his followers. He doesn't inspire them, and they don't trust him. His inability to put himself in another's place is an Achilles heel that literally cost him the world in the Thunderbolts' first iteration. He's a genius, but a terrible leader.
Rick Flag, on the other hand, does inspire whatever nobility he can find in the members of the Suicide Squad. For her part Amanda Waller is utterly ruthless, but not heartless. The Squad knows she will keep (most of) her promises, sometimes too well. Her team may hate her, but they also have the right combination of fear and respect for Director Waller. And speaking of Herself...
4 Ruthlessness: Suicide Squad
In any high stakes battle it pays to be ruthless. While the Suicide Squad may not always be a well-oiled machine, they don't hesitate going for the throat. Amanda Waller appreciates and uses her team's vicious streak. As distasteful as Rick Flag finds this, he supports her, and recognizes the tactical advantage inherent to having a team of stubborn and selfish survivors.
There are a number of ruthless individuals on the Thunderbolts. Zemo personifies the concept and Moonstone focuses all of her intelligence on power and survival. As a team, though, the Thunderbolts have always brought out a compassionate side in each other. Historically, the Thunderbolts stop playing heroes and start living the part. This has its own strengths, but having a heart can be fatal. It can mean not pulling the trigger when civilian lives are on the line, saving them in the moment but losing the war.
3 Experience: Tie
Both of these teams have experienced leaders. Waller has seen thousands of scenarios play out, and Zemo has been repeating his schemes in the endless void of Comic Book Time for decades. While neither team has worked together extensively, a few key players have experience cooperating with each other. Deadshot and Flag have a long history of success. Others, like Harley, have extensive experience working within teams. The Thunderbolts find themselves in similar situations, Fixer having always worked well with Zemo. Moonstone and Radioactive Man are both similarly experienced team players. Finally, both teams have savage wildcards in the form of King Shark and Jigsaw, likely to throw the teams into chaos and unlikely to learn from mistakes. It's a solid draw.
2 Intelligence: Thunderbolts
The Suicide Squad brings a lot of different kinds of intelligence to bear on any problem. Harley's manic inspiration, for example, and Waller's chess player strategies. They don't have any colossal intellects on the team, though, and the Thunderbolts have four. Zemo is a potentially world-conquering genius. Fixer's engineering skill rivals Tony Stark's. Radioactive Man has a PhD in nuclear physics, a perfect match for his power set. Finally, Moonstone's original identity as psychologist Karla Sofen gives her a cold but useful understanding of human behavior.
King Shark's not as dumb as he seems, but that hardly compensates for this imbalance.
1 Winner: Thunderbolts
The Thunderbolts not only have the edge in more categories (4 to the Squad's 3), they also capture some of the most important categories. They have not only more power but also the smarts to use it effectively. The Suicide Squad's superior leadership and ruthlessness might let them win out in an ambush, taking down individual Thunderbolts as a squad. In a team versus team battle, though, the Thunderbolts will also coordinate their greater power well. Zemo may not be an inspirational leader, but he will successfully identify and eliminate threats like Deadshot and King Shark before they can take out key members of his team. The battle ends with Amanda Waller staring at a dead screen, the cold knowledge that Helmut Zemo will quest through omniversal space to find her. His team may not support his decision to come after her, but she knows in her heart that won't save her.