When making appointments to USNA, it is based on geographical location. With NROTC it is completely national.
For example, if you live in a congressional district where you're the only one applying to go, chances are you will go as long as your stats are decent. If you live in a district where everyone wants to go, since there is a limited amount of space per district some highly qualified candidates with 4.0's and 4 years of Varsity Football may not go simply because there is more competition.
With NROTC, candidates are reviewed nationwide. The strongest candidates will get the scholarship even if every one in their neighborhood is also doing NROTC. (College choice has a lot to do with it too) also I saw on a recent thread that the USNA pool is slightly less academically powerful than the NROTC bunch because NROTC doesn't have to accommodate D1 athletes while USNA does. Not to say D1 athletes aren't academically qualified, just that 4.0 2100 SAT lineman are tough to come by.
Please anyone correct me if I'm wrong.