eCommerce makes use of the separate Payment module. The payment module works reasonably well, but we have plans/ideas to improve it further. The basic idea of a separate Paymemt module is that when a payment type gets written, it could be used for any other system/module.
Note that I'm not a core maintainer of the Payment module (at least not yet).
I've created a template to follow for new payment types, which you can find here:
You could also look at the other payment types found there to copy what they have done. Also see:
What payment type will you be creating?
SS 3 eCommerce is definitely on the radar, but no work done or planned at this stage.