The one issue that I have run into is the number of installs. I have a family of 6 Macs, and the MAS version typically lets you install the app on 5 computers, regardless of who uses the computer. The copy purchased from the developer often has different restrictions - some will allow you to install it on 5 computers, some only on 2 computers, etc. Others will allow you to install it on as many computers as you desire, so long as you, the licensee, is the primary user on all of the computers.
In many cases, the MAS version will have sandboxing features that the developer sourced version will not. Sometimes you can work around the sandboxing limitations by giving permission to various functionality, and sometimes, you cannot.
The pricing may also vary between the MAS and developer sourced versions... the developer may offer discounts or "sale" prices from time to time, and whatever you pay the developer for the version direct from him/her/them goes to them. For the MAS version, Apple gets its cut.
As always, YMMV.