I can't tell you every thing I think about that first prophecy, 'cuz I'm saving it for my feature topic, MNOLG Findings (link in sig). I also used to thnk that the stones around Makuta represented the Rahi, Bohrok, Rahkshi, and whatever's left. But now I've realized that it only prophecies the first face-off. Here's why.
The biggest thing is that Mata Nui did not wake up in the prophecy. That's not pointed out enough.
Another reason; in some other versions of that prochecy, there are different numbers of rocks around Makuta, anywhere from four to six. So the number probably means nothing.
And, the prophecy showed the Toa destoying the physical form
of Makuta with a bright light. And that's exactly what happened in the first face-off; Makuta's physical form was destroyed with a bright flash. But, as he reminded them, he is nothing. Which I think means that he is not limited to a physical form; he is a spirit. The prophecy did not
say that the Toa defeated Makuta for all time. It just showed a bunch of rocks, and one of them blew up.
And the fourth reason? Mata Nui did not awake in the prophecy. So it never did foretell everything that was going to happen.
Also, notice that there is no seventh Toa in it. I've got a big theory that relates to this, and it has to do with my feature topic, "What if Mata Nui is all six Toa combined?" but I'm not ready to post it yet.
And the final reason; Mata Nui did not awake in the vision. And he didn't after the first face-off either.
Did I mention Mata Nui did not wake up in the prophecy?