Actually the difference is that Amazon pays you a % of the total sale while ebay pays you a % of their fees on the sale. eBay lowered the fees at the same time!
I'd take 4% of a $100 sale all day long before accepting 6% of a $4 fee on that $100 sale. They did implement a 200% bonus on ebay if your buyer is a tier 1 buyer (new to ebay or not active in 12 months) but that's not something you can build for, it's pure luck(and rather rare).
eBay's current partner network program is one of the least paying in the industry now.