You see that's part of what I think becomes the problem, and why the pros started using MF as support (and unfortunately people in my skill range follow suit without actually realizing what the pros were trying to accomplish). She is so squishy that it begs people to attack her, which just brings them in line to be attacked by the plants allowing her to win a lot of trades. This is countered by MF organizing with her adc to attack at a distance and destroy every plant then engaging. And since there are two ADCs then Zyra just gets blown up from the damage.
So, her design is forcing somewhat unnatural highs and lows, where if certain team comps are opposed to her Zyra can't actually do anything, while if the enemy team comp isn't one of the handful of combinations that can methodically get rid of her plants before taking advantage of her non-existent defenses they have no real counter-play to speak of.
Honestly, giving her a tad more defense while cutting not her initial skill-shot damage, but her persistent plant damage could balance that out a bit. It would allow more time for all enemy team comps to deal with the plants, while allowing Zyra to not die because the enemy sneezes in her direction.
Of course, this is just arm-chair game design from an unranked player. So, take everything I've said with so much salt it becomes inedible.