In the Project universe, where would you see Zyra?
For me, while thematically, it would probably make more sense for her to be on the Program side, having her turn into some motherboard AI that wishes to spread technology, I'd love for Riot to reinvent her character, like they do for many other champions when they get skins. Take GodKing Darius for example, in the actual lore, Darius is a disciplined warrior, caring only for Noxus, and is even one of the 3 rulers of Noxus, while God-King Darius is a complete departure from this, being a total anarchist, and wanting little else but destruction.
Zyra, at her core, has always been about growth, and the primal animalistic nature, which is the complete opposite of technology. Making her Project instead Program, even in a universe that's dominated by computers, would make her seem far more human, and probably even more human than how she appears in all her other skins. Maybe shift her want for growth of plants for the want of growth for humans. Have her be a scientist, or some sort of coder, who wanted the advance of technology to help the growth of humans, but after falling to Project, she's seen the light, and work for G/netic, using the very technology that she helped create against the enemy, similar to Resistance Illaoi.
I know this is all hypothetical, and considering Zyra doesn't get many skins, due mostly to her very detailed design, but if Zyra were to ever get a skin in this universe, I hope it's Project, and not Program. Also, this would probably be one of the easier themes to use for Zyra, transitioning her vines to wires, and her seeds into mechanical cores.
Also, this is just a side note, but if Zyra ever gets a lore update, I just want Riot to know that what a champions uses as their "weapon/magic" doesn't always have to be the focus of their story. Kinda tired of every plant related character just being a Poison Ivy knock off that only wants the spread of their "plant children."