After Siegel, Edmond Hamilton took over for a bit, in the gap between Siegel and Jim Shooter.
Hamilton's short in-between run brought us "The Legionnaire Who Killed!" (ADV #342), where Star Boy is tried for breaking the Legion Code, albeit in self-defence, and in a quite remarkable twist, is not given a reset button but actually expelled from the Legion. He rejoins some time later.
This was followed by "The Evil Hand of the Luck Lords!" (ADV #343), which is a typical "mystery" Legion story, but features some nice art by Curt Swan and sets up the Luck Lords which would appear later in Legion lore (and most recently in the first arc of the new The Brave and the Bold comic).
Then there's the two part Super-Stalag of Space story, "The Super-Stalag of Space!" and "The Execution of Matter-Eater Lad!" (ADV #344-#345) which is actually a pretty nice pastiche of the movie Stalag 17, although it ends on a rather odd note, that of Matter-Eater Lad becoming overweight due to an altered death-ray filtered through Superboy (don't ask).
And finally, along came Shooter, with "One of Us is a Traitor!" (ADV #346, Jul. 1966) and "The Traitor's Triumph!" (ADV #347, Aug. 1966), introducing Karate Kid, Princess Projectra, Ferro Lad, Nemesis Kid and the Khunds. Not bad for a debut! It's marred a bit by his amateurish layouts finished by Shelly Moldoff in Part One, but Part Two has Curt Swan returning to clean up Shooter's layouts, inked by George Klein. And a new age is born.