Well, asides from REALLY Samsung-specific apps (like an S-Pen enhanced version of Twitter, Evernote, Sketchbook, and Samsung proprietary apps) I find that Google Play has the same content as Samsung Apps but the same cannot be said the other way around.
Also, most of the time devs update Google Play versions but neglect (if not forget entirely) 3rd party store versions, especially Samsung's. I've used Soundhound and Evermondo from Samsung Apps and then just watched as the Google Play version kept updating over and over again while I was stuck with the same bugs that others had already fixed. NOVA 3 is also a good example of different versions between stores.
However, Samsung does give some very good apps for free with new purchases, but only if downloaded from their store. And just like Amazon's free app of the day, sometimes they give apps away for free and that makes it appealing to download their version instead of Google's. But if you gave me a choice, I'd go with Google Play.