I think the analogy is someone shuffling a deck of cards, and taking a peek at the first card. Then betting someone $20 that it's the ace of spades. The process is justifiable, because you don't have any control of what the top card happens to be. It's just that you know what card it is and wouldn't make the bet if you didn't know it was already an ace of spades. Similarly, Curve25519 might have been constructed and happened to have the "one-in-a-million" vulnerability. How many other "Curve25519s" are there that we didn't hear about. Imagine that instead, the procedure was shuffle the cards after you commit to the bet.
I really doubt there's anything wrong with 25519. I feel like if anything, if djb et al knew about some vulnerability in curves that 25519 happened to have before releasing it, they would have put the weakness as one of the failing criteria to pick a new set of parameters.