Throwing it out there that it would be a very interesting idea if he didn't approve of Balance and Riot actally gave the Ninjas someone to oppose. He also seems to have a Ninja army and Ionia needs more characters that aren't "Good" or follow the philosophy of Ionia. I mean the other factions have characters on both sides of the fence, right?

We already got Syndra and Varus for Ionia

Morello already confirmed that he's an antagonist working against the Kinkou.

Yes, this is perfect! Now the Ninja Trio has a real enemy that actively acknowledges them!

Oh this feels like Power Rangers! If only they had 2 more rangers... Unless Syndra and Varus are corrupted Rangers!

Go Go Mundo Rangers!

(Mundo is totally Zordon. Or Alpha-Alpha)

No, Corporate Mundo should be Zordon. He would be the best boss for the Ninja team.

Demacia believes in justice and order, and Noxians believe in freedom from control, and the ability to seize power for yourself. Kayle's family believes pretty much the same thing as Demacia, and Morgana believes pretty much the same thing as Noxus. There has always been two sides of the coin, so to speak. So if the Kinkou Believe in balance, it would make sense that Zed strives to ruin that balance. But why?

Maybe Zed saw the darker side of the Kinkou. They are neutral. They sometimes to morally questionable things to preserve the balance. It would make sense then, that something they did to keep balance, ruined Zed's Life. Maybe they killed someone he cared about, causing him to slowly fall into darkness.

Another possibility is he could have been part of the Kinkou, but was kicked out due to breaking their laws, only to be replaced by the new three. Once again, this gives him motive to try and end the Kinkou's efforts.

In the end, this post will probably mean nothing, as i'm sure Riot already has the lore, but it's still fun to guess.

Zed is Shredder
enemy of a ninja group
hand claws as weapons

Would be nice if Akali is secretly on Zed's side. Fist of Shadows, Master of Shadows? seems like a connection.

Syndra and Varus are confirmed not to be tragic villains. Syndra's a grown Annie with inmense magical powers that she wants to test out around. For that, you cant really call her "evil", even tho she just killed the master that tried to seal her magic. Neither is Varus a bad guy, since he sacrificed his belief and obtained dark powers to fight back the noxians.

Zed, however, believes on a darker path and thinks on eliminating people that opposes him. While the path of light and dark can be justified, Zed's way of doing things are not "right". So we can claim he's the very first 'villanous' Ionian champion.