You can't step on her seeds. I had to walk over it four times before I hit it and by then it was so long that it was pointless to even have tried.
Fix this stupid bug.
You sir have indeed discovered a bug! At some point the particle and sound alerting opponents that Zyra's seeds are now stompable started playing when the spell was fired, rather than when the seeds indeed became stompable. I just promoted a fix for this. Hopefully it will be out next patch.
As to your assertion that quickly stomping seeds is skill based, I suppose you are somewhat correct in that it would require Zyra players to position their seeds in awkward locations, which would in fact take some getting used to and would require more mouse micro. That sort of mini-game is not what I was actually going for when designing her.
The seed stomp mechanic is actually designed to do two specific things:
1. It limits her soft zoning capability -- where she zones you through the threat of plant activation, rather than by committing to activation;
2. It limits her ability to grant 30 seconds of uncounterable vision to of an area to her team.
Skill requirements are not virtues in and of themselves. Had I had wanted to add more skill to Zyra, I could have also given her bonus damage when casting a spell in a direction she was not previously facing (requiring clicking behind her) or perhaps added extra damage if she damaged an enemy during an odd second (e.g., 2 min 13 seconds), but less damage if she did so on an even second. There is no limit to the amount of "skill requirement" a designer can put onto a champion. Skill tends to play out not as a good in and of itself, but as a means of supporting a play pattern, of enabling counterplay, or of making game actions feel meaningful to the player.
Instead, I built the Zyra skill cap along three axes:
A) Positioning: Zyra is the slowest champion in the game, tied with Anivia, who also is 300 ms with no movement speed increase and one of the most fragile as well. If she makes even a slight misstep, she can be punished severely;
B) Targeting: Zyra has no targeted spells, all skill shots and delayed detonation abilities, so she can miss;
C) Execution complexity in her skill combo based on coordinating locational seed placement with ability timing. Given that I tend to cringe when I see pro players use Zyra, I may have gone overboard on the difficulty here -- it's actually very tough to put one's seeds in the optimal location and trigger them as the optimal plant while hitting your opponent with the base spells as well.
I've attached an image showing the simplest example of point C.