I just noticed that humans invented clothing in Genesis. One thing God didn't think of, or didn't expected humans to think of. Either way, humans came up with it by themselves.
I always considered the apple a metaphor for education and, dare I say it, science. God had a monopol on knowledge and eternal life in his self made garden. He is described wandering through the garden for his own amusement. Once humans tasted the apple, they became self aware, educated and - most importantly - developed free will. God became angry when they covered themselves, and he wanted to know who told them that they were naked (still assuming they didn't realize that themselves!). And then, afraid of them also tasting from eternal life, he punished and exiled them.
Not to forget about the snake, which revealed the death threat was a lie. God had no control over the snake. Design flaw? Beyond his powers? A part of the character test (but God punished the snake as well, so that's another vote against that theory)?
It's basically a metaphor for regimes trying to keep you illiterate, and considering you a threat once you become educated, draw your own conclusions, and make up your own opinion.