Minimum invoice amount
I received an invoice of $1 and was surprised Mailgun makes a profit out of this after all costs of administration and support. A client of mine received an invoice of $0.80.
Sure you can do better than this!
I don't mind that you turned the Free plan into a Flex subscription. But the way you do it is a heavy workload of bookkeeping and administration.
Other than that, I love the product.