One aspect is the speed of evolution - as one species evolves, its competitors evolve just as much, making it difficult to dominate too much. This is a limitation that GM does not share - it can make genetic leaps in a few years that would be vanishingly unlikely to occur naturally, or would take millions of years. Other species could not keep up.

To illustrate with the previous example, insects evolve resistance to the chemical countermeasures that plants evolve. But give those countermeasures a GM kick, and insects won't be able to keep up. I'm sure eventually they would evolve something, but there could still be a huge crash in their population before that happens.