My top issues running my business on Stripe:
1) Many countries still only allow depositing a single currency (i.e. Aus/AUD), doubling the cost of transaction due to the currency conversion, even tripling when we have to convert it back to pay our bills. I always get told either "soon", or "not possible due to the law", despite competitors doing it.
2) If we were an EU company, we'd get charged 1.4%+25c on transactions in the EU, where most of our customers are. Instead, because we're selling from Australia, we get charged 2.9% for some arbitrary reason. This coupled with 1) puts our all-in transaction fees at 5%+ :(
3) I think billing the vendor for refund fees is a really retrograde step - it increases friction in the decision for us when a customer asks for a refund, and industry wide is going to cause less happy customers and less card users online. It's already hard enough convincing Dutch/German customers to use a credit card online.
If any non-EU companies know a cheaper way to process transactions in the EU, I'm all ears...