Points to consider:
1. How much do you NEED in terms of storage? The Samsungs give you the option of a 128GB external SD card. The main reason I tend to stay away from Nexus tablets is the lack of the expansion slot, due to the fact that I have an every growing library of ebooks that I tend to need to keep around at all time (working at a hospital). If you tend to want to keep a lot of movies or videos that aren't streamed (DVD/BlueRay rips), you'd want the extra storage.
2. Performance. Overall the Nexus should perform better, even if they'd have the same specs due to less overhead (less bloat, no manufacturer skin). However, for usual tasks they should perform roughly the same IMO. At this point in time, the Tab S series is the best spec'd non Nexus tablets, mainly because they're the latest release from the manufacturers at the high end. You can probably wait for Sony's new Xperia Tab, or LG's next G Pad, but at this point, if you're looking at performance, choosing either won't matter much IMO.
3. Screen. Not about size. They're close enough to not bother, especially since the onscreen navigation bar on the Nexus effectively reduces screen size on several instances, but the Samsung has the keys completely off the screen. Although some prefer one option over the other. However you should consider that the Tab S uses AMOLED screens. And well, those either you love them or hate them screens.
4. Updates. Obviously the Nexus gets updates faster, and has a longer support time (hopefully. The Nexus 10 debacle was crazy).
