much of intuition is made, not innate, at least for things as abstract and arbitrary as languages and notation. If you come at this question from a point of view where an array is a block of memory words indexed by a pointer - which is pretty much how system programmers back in the day when I did such things, 50 years ago - then zero based seems natural and obvious. The pointer to the array is the array, and the first element in the array is the pointer plus zero, the second, the pointer plus one, and so on. Once you start thinking that way. For multi-dimensions, the arithmetic just falls out as well.
But I don't think the fact that many of us developed that intuition, makes it inherently better. It just makes it more intuitive for those of us who developed that inuition. I've written oodles of codes with both paradigms. Either works. Zero is just more natural, to me.