The Master is a must, but has to have a great storyline to bring him back to being a real threat. Ruthless. Alpha always needed more powerful villains. No more wax figures or robotic versions of other heroes.
I found a big problem is Flight over the years was that the heroes were so powerful that lazy writers had to get rid of some characters just to be able to give them a challenge. The Baubiers are like having two Rogues on your team. Sas was like the Hulk. Mac and Heather were like 2 Iron Men. Snowbird, semi goddess who could become any animal and had some powerful friends "upstairs". Shaman is like Doc Strange but can also pull anything out of his pouch. Box a huge robot that could become anything and the guy inside is basically a good guy Magneto. Persuasion just had to talk! They had all their bases covered! Try to think of a threat that couldn't be smashed, shot, flew into at his speeds, blinded by light, attached to the ground by vines, dropped a car on or simply told "um, don't do that".
One good thing about having such powerful heroes is that if any of them turned, they'd each be a great villains!
Poor Madison Jefferies has been brainwashed so many times. Just having him on your team is like having Magneto. He can maniuplate Metal, Plastic and Glass. His brother could manipulate human tissue(come on, he blew up. His power was to manipulate tissue, he could pull himself back together, right? :P ). Imagine the Jefferies brother working together. They'd be almost unstoppable. Yes I like Madison but if he's not going to be used as a hero he might as well be used as a villain!
Persuasion can manipulate people's actions with a single word. She was too powerful to be on the team cause she could just say "sleep" and the battle would be over. Imagine a villain using her to his advantage. What if Brass Bishop had her chained like that Dargil (whatever his name was) in V2. Use their friend against them in a powerful way.
Flex. For god's sake he's T-1000 from the Terminator! Completely unstoppable! He can turn into anything. You can shoot his arm and it'll grow back. He could hunt and chase people down and rip through anything in his path.
Witchfire is basically Pheonix meets Scarlet Witch. Nuff said.
You want a worthy team to fight against, look no further then former members. It worked in the original and would be a nice tribute if done correctly.