I've been using wpec with gold cart and atahualpa for a while now in my shop
and use PayPal for payments.
I was very happy with the look of the site using ata and after a lot of tweaking and months of frustration with various updates, it does function quite well. However the old versions of wpec don't have the means to seo your site easily without hacking the code so that has had a serious effect on my site's sales and still is. It is also very tedious, slow and laborious to edit when you have a lot of products.
The new wpec 3.8 + versions promise to use wp's seo features and so I was very very pleased when it came out to update to the latest versions.
Unfortunately the update completely screwed my atahualpa site up and left me in tatters. I am not a coder and to solve my problems have been regrettably forced to change to weaver (as the older wpec versions arn't worth fixing or asking for support now the new ones are here).
However, now using up to date versions of wp, wpec and weaver and gold cart I still have imaging problems that have left my new test sites unuseable and am also unable to use a product importer because of these imaging probs which would potentially massively speed up my sites efficiency.
Wpec is excellent in many respects and if you use the right theme and that theme fits your needs then you have a winning combination as long as you can mess with code a bit and personalise your shop.
If like me and many others, your themes don't work, you can't fix them and have no money to throw at the situation, then you''re in deep trouble and have to try and get support from the forums, which can take weeks with no guarantee of support at all.
I wish atahualpa worked with the new wpec as it did with the old. Proper integration would be amazing for thousands of potential shop owners I'm sure.
I bought themeframe in the hope I could use it but haven't tried yet. If that integrates well then I'll be one happy man.
All in all, wpec is a double edged sword. It's either amazing or a nightmare. However it is improving all the time and I'm sure one day it will be the solution for all wp shops. I just hope themeframe is fully functional with it as that would be an amazing and probably unequalled combination.