My assessment (which may be biased) is that Floris has more stuff all around and, crucially, all of the Warband staple mod features (Custom Commander, Diplomacy, Freelancer/enlisting, and I would hope to venture the tactics/formation features of Pre-Battle Orders & Deployment), but that Native Expansion has a bit more of a cohesive feel to it at the moment. So if you want more sandbox--more items, troops, graphics, gameplay features--do Floris. If you want more quests, the challenge of the invasion, etc, do Native Expansion. Both remain in development, each (in my mind) trying to move toward the 'middle', with Floris working on quests, balancing and polish, and Native Expansion bringing in new features.
Wouldn't hurt to try both, or to take a look at their feature lists and see what catches your attention.
I'm fairly certain Native Expansion hasn't been updated for a while.
They just came out with a new beta version or currently in the process of doing so.