We are working on the ability to specify more than one kind of variant, and you should see this in a couple of months time. You can add up to 50 variants, so it is possible to have combinations - for example. Small, medium and large Red, the same in Yellow, and again in Blue. This would only result in nine variants.
There are no current plans to add alternative payment gateways, due to the heavy integration with Paypal, but this may be reviewed in the future.