My colleagues and I have had issues with ebay in the past. And being that sites like ebay and amazon survive off fees mostly it will be interesting to see how they adapt or fall off as bitcoin becomes more mainstream and then more preferred as a payment option. Though this is probably another five years away or more. I am really hoping both ebay and amazon choose not to accept bitcoin for a long while; which will hopefully allow other smaller start-ups a decent share in the market.
Amazon has no reason not to accept Bitcoin payments. But the case with Ebay is different. A lot of opposition will come from Paypal, if Ebay accepts Bitcoin as a mode of payment. A compromise might be reached in the end, I hope. Probably Paypal will also integrate Bitcoin to its system.