Indeed the Wikipedia article doesn't paint it in a great light. The system itself seems to be quite old, but I'd love to see some serious studies of it. The only thing I can add here is that our understanding of human mind is really basic at this point and we have to wisely balance between what we can already measure and our intuitions. That's how all sciences evolved.
I understand your point about classifications, but it assumes that Enneagram spectrum is a result of random distribution of X values in some vector. In such case indeed each dimension should have 2 extremes. However, according to my vague intuition Enneagram is somewhat different. Rather than describing the whole space in which each solution (personality type) is equally possible, it seems to describe specific points in the space that seem to act like attractors. For some reason these specific behavioural patterns crystalize, because they tend to create very specific meaning/identity and way of making sense of the world around us. You can't create an identity/self around 'lack of something', it needs to be some specific quality that allows to interpret reality in given fashion.
The example you bring up (type 1, the Reformer) is not about reforming vs not reforming, but rather about seeing the world in terms of perfection: this is perfect and this is not perfect. Hence they may end up as a reformer or just someone overly pedantic. Other types have completely different perspective (eg. this is safe and this is not safe), so in a way each type is a separate according to which a given person interprets the same reality.
This is very subtle and more complex than M-B. In M-B we have one 'objective' world and set of values in which various types rank differently. In Enneagram each type has a different way of defining the world/experience so in each case the measuring axes are different. It's as if you had different formal systems based on different axioms - each would end up with different consequences and you wouldn't be able to compare their statements directly. You'd have to compare the properties of the systems as a whole.
Your last point about infancy - that was my mistake, I shouldn't write 'early childhood' (edited). The theories I heard mentioned some formative, sometimes traumatic (single, or repetivie) experiences in childhood/adolescence that shaped given perspective.