I requested a replacement for my crushed Persona 2 as soon as it became available again on Amazon. Of course they sent it in another bubble mailer and it was crushed again. It's kind of surprising that they would continue to ship these in a bubble mailer after all the complaints they got. They only difference for the second shipment was that it was delivered by A1 Courier rather than UPS.
I put in a request for yet another copy. If it arrives crushed again, I'll give up and ask for a refund.
I had the EXACT same problem you had. They shipped the first copy, game box was crushed. Got the replacement, the game wasn't as bad, but still crushed. I called Amazon's CS, and told them of my problems. The guy said:
A. "We'll reimburse you for half the cost of the game ($20), while keeping the replacement." or
B. "Put in a request for another copy."
I chose A, since only the bottom flap was bent, and not the rest of the box like the first copy.
I would definitely contact them about it.