Don't know anything about Nations, but as a travel team, we played tournaments with a whole bunch of different sanctioning bodies. We played USSSA, Triple Crown, BPA, CABA among others. The problem we had with USSSA was roster restrictions.
We had a situation where we played a tournament early in the spring. We did not have our roster set (in our minds) as some kids were still playing school ball and had not given us an answer yet (we were a 14 yr. old team). Anyway, we played in this tournament, lost in the 1st round of bracket, came in something like 5th place. Top two teams were to be given a World Series berth. When you earn a berth, I think you are allowed 3 roster changes. Well, apparently three teams who finished ahead of us had already secured a berth, so they gave one to us. Never even told us. Coach was making some changes later in the year and got locked out due to the roster restrictions. They would not work with us at all. We even told them they could take back the berth and we would re earn it again. NOPE. We were stuck and basically couldn't play any more USSSA tournaments.
If you are anticipating any roster changes during the year, be careful about entering an early USSSA tournament. You may fall into a berth and a roster lock out without actually "earning" a berth.
On the other hand, USSSA is the only organization that I know of that keeps track of their tournaments, schedules, assigns a point system and ranks teams. That is pretty cool. Only drawback is the roster restriction especially early in the year before you are all set.