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A friend of mine saw Les Paul play at the Iridium in New York and asked him that very question.
There where 3 technical factors.. and 1 funny one.

1. When he did fast runs up the neck, the bottom horn always got in his way.
2. He hated the neck.  He thought they were flimsy and not as stable from a tuning stand point.
3. He liked the Mahogany body - maple cap construction of the les Paul better from a tone standpoint. In fact that's the same thing he didn't like about the old Les Paul Customs.
4. He didn't want to do anything until Mary was out of the picture ( so she couldn't get part of the contract money).