Using a few fee calculators & testing with a $100 item, it looks like they're comparable if the seller isn't using FBA. But, assuming FBA, then yes you spend a few dollars more than Ebay for the same item. However, selling via FBA can also give you a boost in sales with customers more inclined to buy when it will fit in their Prime subscription, and that increase in sales may outpace the increased cost.

Also, at least based on my own buying habits, (I know hardly representative) I'm much more likely to feel "safe" buying something on Amazon. But either way,to hit the most audience and maximize global profit, you can simply sell in both venues. Given some of the sales management tools that let sellers manage inventory & pricing across platforms, it doesn't have to dramatically increase the overhead of a sales & fulfillment operation.

As for switching from selling wholesale to Amazon to Marketplace, it may actually result in a net increase in profits because it is probably likely that selling retail via FBA will get more money in the sellers' pockets than the wholesale cost.

It really would be nice if Amazon gave sellers more certainty in this process though. It sounds like details & timing have yet to be fully nailed down, and it's the type of change that a business should be given something like 6 months of advance notice.