It may not be “that bad”, but it’s still enough to be daunting if you’ve been in full-swing development mode and would rather focus on your application’s key features instead of licensing and distribution.
That said, I have apps on the Mac App Store and though it’s effortless, there are absolutely points of frustration. Most notably, there’s no way to refund or interact with unhappy users or users with questions. Additionally, OS X's sandboxing implementation is still buggy in some areas (mostly involving file dialogs and persistence of user-selected file URLs) which makes writing and usage of applications that frequently work with files in arbitrary user-selected files and folders in the user’s filesystem far more frustrating and failure-prone than it needs to be.
As such, I’m looking into moving into self-managed licensing, with a setup like you’ve mentioned (Sparkle/CocoaFob/etc) but rather than using Fastspring, I’ll probably use a personally maintained branch of Potion Store that supports Stripe instead. I’ve never been a fan of in-betweens like Fastspring as a developer or as a user; as a developer, I dislike the lack of control I have and as a user encounters with Fastspring and the likes feels janky, unpolished, and unprofessional.