Legion of Super-Heroes (TV series)/WMG

Bouncing Boy resigned as 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.

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: 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.
 * 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.