We moved to J2Store. There's a lot of really good checkout extensions out there now like HikaShop, K2Store and others that are a big improvement over what we were using before. We ultimately settled on J2Store for a few reasons, including developer support and subscription/download handling, but each site has their own needs. I wouldn't say J2Store is the best payment extension for all cases, but it's a good one that's flexible for a lot of uses.
We're still working out a few kinks in the upgrade, honestly, but when that's done, we're planning to create a blog post announcing the update along with some learned experiences
Thanks,
Alex