Final conclusion:
-Mata Nui was not the only Great Spirit built.
-Another Great Spirit crashed at the same time of Mata Nui's creation (100,000 years ago) on a planet called Bara Magna and caused a planetary catastroph.
-This catastroph destroyed the inhabitants' sources and technological achievements.
-Plus, the beings living around the region which is home to the Vorox and Zesk got in contact with mutagenic substance which leaked out of the Great Spirit's damaged, dead body and got mutated.
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Oh, I forgot to add something- if this "robot" had the same mission as Mata Nui, perhaps the Great Beings had to build Mata Nui because the robot who was supposed to accomplish that mission was destroyed, so he would indeed be, like you say, a prototype. This would also explain why the Great Beings made so many preparations for the case that Mata Nui was somehow struck down- because they didn?t want a second Bara Magna catastroph (and they were too lazy to build a giant robot again ).