My theory: it wasn't the plants.
This movie is pretty damn bad, but I do think brief glimpses of Shamalan's genius shine through. Easily my favorite element is one that is often overlooked; its ambiguity. While most of the characters in the film seem to agree that plants are the culprits of this apocalyptic attack, I disagree. There's the theme in the film that science can't explain everything; multiple times in the film is this line referenced, and Mark Wahlberg even says at the beginning "scientists will have their theories for the books, but it doesn't mean they're right...somethings are just beyond our understanding." The fact that the film bookends itself with this statement at both the beginning and end shows that this is obviously something symbolic of the meaning of the film.
This implies that, even though people have reasons to theorize the plants are behind this whole thing, the theories might all wrong and it could be something else entirely. The movie loves focusing on the sky, especially during the opening credits. The very last shot in Paris seems not to focus on the plants, but rather the sky above the plants. In fact, rarely at any point does the cinematography focus on any plants, flowers, trees, or grass at all. You'd think a film about killer plants would show at least a few closeups of ominous looming grass, trees towering over people, something of the sort, but it never does. To me, this can either imply multiple things:
1. It's global warming, or something similar. This one is a bit obvious and lots of movies have done it, but it could just be Earth's way of giving us a wakeup call.
2. It's a religious event. Shamalan loves referencing God and Christianity in his films, with the theme of Signs being that God acts in mysterious ways and that all things happen for a reason. Perhaps the focus on the sky implies that this is an act of God. The whole "beyond what science understands" thing definitely reeks of something religious.
I also don't think the plants are the villains (what an odd statement) because the film constantly mentions the bees dying off. Bees are plants number one friends, so why would plants be killing off the things that keep them pollinated and alive?
Overall this film is terrible but I do think it could've worked with a few more screenplay drafts. Shamalan bragged about the film being written in one go and it clearly shows. Some of these more subtle ideas could've been better realized with two or three more drafts. Or, it should've been a full-fledged horror-comedy, like Tremors or Slither. In the end, I do think the plants are not to blame at all, and I think Shamalan intended for us to discuss the film's many mysteries, but too bad the film sucks and nobody cares.