Her W is a one point wonder ability anyways. It isn't the first ability you should be maxing, nor should it have had a strong incentive to make you think otherwise.
You're trying to make two comparisons that aren't equivalent. The first being that you're comparing Zyra, a zone control and CC mage with some supportive tendencies, to an AD assassin and AD melee carry. Different classes have a different general design that they follow. A better comparison would be one between Annie, Morgana, even Anivia. The first two of those three are in the same position as Zyra (Mage as primary role, but generally played as support). Anivia has zone control and CC tendencies like Zyra. Know what they all have in common? None of them get bonus AP/MPen built-into their kit.
Second, you're making the assumption that AP and AD are equivalent stats when they're far from it. AP is far easier to stack where AD values get to be about 50-75% of what AP values hit. AD adds power to auto attack damage, where AP does not do this unless there is a built-in on-hit effect on a mage (rare). Tying into the first issue, AD, AS, Ar Pen, etc. function as built-in kit steroids on carries that need them in order to amplify synergy with big ticket items like Bloodthirster and BotRK. AP is not a steroid; it's a stat that you need to build towards because of how mages work; high bases and burst effects on their spells compared to spells from other roles.
Finally, to elaborate on my post, if you need to add built-in AP to a champion's kit, that's literally just adding flat AP, because "needs more burst", you may as well just add more base damages to the abilities, because that accomplishes the exact same effect with far better clarity. An AP% extra effect could be interesting, but is overkill on Zyra and would have obvious ludicrous synergy with Deathcap. Built-in Mpen should be a special stat on few champions, which again, isn't needed on Zyra. If you're interested in fixing her damage, go for something simpler that fits with her design, like her plants. Have W buff her plants with levels, so add something like:
Rampant Growth:
Plant Damage: 23 + (6.5 × Zyra's level) + 20/22.5/25/27.5/30% AP
Plant Health: 6/7/8/9/10
Would be far more thematic, and less "bandaid fix"/nonsensical than throwing in random AP/Mpen that no other mage gets just for free, randomly.