1) No direct paypal integration in the cart, user goes to paypal to pay for the item. 2) no direct google checkout integration in the cart, user goes to google checkout to pay for the item. 3) No way to track affiliate sales due to #1 and #2
However, I love our custom site, better than any off the shelf shopping cart.
Anyone know what shopping cart allows the above, but we can still use our custom site?
We can just "post" the data to the cart. We'll still host it.
With the amount of work you'd have to put into integrating something new, why not just build the extra functionality that you need into your custom cart?
I've been thinking of offering paypal as a payment option and just had a quick look at their api, it looks pretty good, as long as there's a couple of hooks in the commerce site you built in house it could be easier to add functionality rather than integrating a 3rd party option.
Failing that, you might like to look at foxycart as a solution because there is an emphasis on integration, I haven't used it pesonally but a friend of mine has for the last year or so and is quite happy with it.