Ko Ni was shot in the back of the head in late January in broad daylight outside Yangon's airport while waiting for a taxi with his infant grandson in his arms.
He was a vocal critic of the army's lingering grip on power under Myanmar's new elected government and Suu Kyi's party has branded his killing a "terrorist act" designed to thwart their policies.
The gunman, Kyi Lin, was arrested at the scene after also shooting dead a cab driver who tried to stop him escaping.
Kyi Lin and Aung Win Zaw, who allegedly paid him to carry out the killing, were also charged with possessing an illegal weapon, a court official told AFP.
"We are standing for justice for U Ko Ni, who was assassinated. We are working for justice," prosecution lawyer Nay La told reporters, using an honorific.
Two of the men in court were ex-military.
A fifth man accused of ordering the killing who remains on the run also has army ties, fuelling suspicions Ko Ni was murdered for trying to abolish a 2008 constitution.
The charter, brought in under Myanmar's former junta, bars Suu Kyi from becoming president and enshrines military control by guaranteeing them a quarter of parliament seats.
But commentator and friend of Ko Ni, Bertil Litner, said it was "common knowledge" that the lawyer was close to finding a loophole.
"Ko Ni told several people, not only me, the same thing: it's useless to try to change or amend the constitution because the military controls 25 percent of all seats," he said.
"But there's nothing in the 2008 constitution that says it can't be abolished by a majority vote in the parliament."
Military officials have denied having any part in the shooting and pledged to bring the killers to justice.
(This story has not been edited by Business Standard staff and is auto-generated from a syndicated feed.)