I think the key would be to find a company to partner with (say Krogers?) that would, with the customer's approval share the data from their loyalty programs that, in theory, store it.
This way the customer only needs to take one action, opt-in when signing up for the loyalty program, as opposed to scanning a barcode or QR code for every purchase.
One way to minimize the compatibility issue with existing software, is create a (hardware) printer (generic), that print on screen, and generate the barcode so the user may scan.
i love the part of "integrate with an on-line personal finance". there are also some legal issues.
bring it on!