I agree, this feature would be of IMMENSE and immediate value when billing clients if only to encourage them to use a less costly payment method. I'm thinking of a feature that allows you to toggle billing the customer for various transaction fees and automatically adding that to invoices during payment based on the payment method that the customer chooses to use. Implementing such a solution by hand becomes time intensive with enough volume and error prone.

2.9%+.25(per transaction) off of gross sales is a significant piece of over head at scale. I just joined QuickBooks in lieu of other Bookkeeping Software because of the affordability, scalability, and integrated products/services (one of which being online payment processing). However, without this feature I'm inclined to find another service that has this feature and integrate that into QuickBooks. Bit of a hassle and I'm shocked that QuickBooks doesn't have this. I hope the feature is on the docket for development!