WMG / Legion of Super-Heroes

Bouncing Boy resigned himself from leader.
Out of guilt for Ferro Lad's death.

The Controller will return to menace the Legion as the Time Trapper.
The portal Superman sent the Controller through took him far into the future, to the End of Time. There he found the Library of Time and learned all he could about the timestream and ways to manipulate it in an attempt to destroy the Legion. He may have caused the "great crisis" that was occasionally mentioned.

In the original comics, the Time Trapper was revealed to be a Controller, until retcons and reboots gave him Multiple-Choice Past.

Timber Wolf's father in the show isn't the real father
In his debut episode, TW showed the team a picture of his father and he looked rather kind. He has the ability to clone himself as in a season two and from season one, genetic engineering. His clone killed him, took over his life and just grew evil.

Timber Wolf's mother
Timber Wolf's mother died long before the series began from unspecified circumstances (like in the comics), Dr. Londo never got over his wife's death and he altered their son so he doesn't share a similar fate (if she died as a result of illness/accident) or for revenge (if she was murdered). Though as time went on and his mental state worsened the motivation for experimenting on their son became more skewered before it ended up being a pawn for his army/scientific achievement/hitman for hire or what not.

If handheld cameras are still around in the 31st century, she took the photo of Dr. Londo and Brin, Londo kept the photo with him because it reminded him of a 'simpler' time when they were happy and together as a family or just a reminder of his wife

Superman and Brainiac 5 would be distant in season 3.
After becoming organic and Brainiac 1.0's influence gone, his man-crush for Superman is gone with it. The "man-crush" is actually a perverse part of his ancestor passed on to him. What he thought was admiration was actually subconscious analyzing to plan for Superman's downfall. Brainiac 5 also fears being near Superman again will just bring back painful memories.

If the show had continued, Kell-El would have become Drax
A few points:
  • Drax mentions he was designed to be immmune to kryptonite.
  • He hates Superman for something that hasn't happened yet.
  • A dual voice is heard in Drax's head at one point, reminding him of why the voice's owner designed him.
I'm guessing that in the next season Clark and Kell would have had a falling out (maybe over killing Imperiex or something like that), Kell would have gotten really pissed off, and the Legion would trap him in the Phantom Zone because he's too powerful for a normal jail. After a while in there, he just doesn't look the same anymore at all.

Bouncing Boy is the descendant of the Teen Titans
Considering he's a superhero from Earth and he has Robin's spiky black hair, leadership qualities and tendency to date girls with miniskirts...

Brainiac 6 would have been a Non-Action Big Bad and would have formed a Five-Bad Band or a Quirky Mini Boss Squad.
After his resurrection, the body of Brainiac seems weak. If the series had continued, Brainiac would have hired several villains, to serve as his muscles.

Possibilities: Fatal Five (except Validus) and/or Legion of Super-Villains.

Brainiac 5 has a Flying Brick fetish
His relationships with Supergirl & Andromenda in the comics, plus the Ho Yay with Superman in the cartoon. Do the math.

Or he just likes smart people
The other members with the highest intelligence are Superboy, Supergirl, Invisible Kid, and Dream Girl. He's been connected with every one of them (Invisible Kid was hinted in the reboot, Dream Girl in the threeboot).

Cosmic Boy would join the main team to be more humble and less strict.