Hi, thanks for trying out Joocommerce and it's great you like how it looks & works! As we say on the website and in the JED description, we support PayPal as the only payment method;
About the shipping methods, that is something you add to the store settings based on your needs / location / deals, and they can be configured price-based or weight-based. I'm sorry you didn't 'get' how they work from the interface and the guide, it means we need to improve the documentation.
As for product variants and options, we have them in plan for an upcoming release!