Apple taking 30% of the proceeds is a big issue I believe, and from what I saw a few months ago in a news article, a developer of a popular app wasn't really getting a lot of revenue.
As already mentioned, Apple imposes restrictions on what APIs can and cannot be used, Applications like Carbon Copy Cloner and other do not fit too well with those restrictions.
Also consider the fact that the MAS doesn't really have any sort of upgrade pricing model, or a demo type of setup
Then there's Apple's inconsistent review process which can hold up the release of an app, or reject it, even though they may have approved an early version with the same feature.
The Windows store is much weaker then Apple's and it hasn't really captured the hearts of developers. I don't know the details and policies of the windows store, so I can't say its worse, the same or better then Apple's MAS.
The MAS definitely has some advantages, as its easier to get your computer up and running, i.e., your apps can download from the MAS when you buy a new computer (or wipe your existing one).