In terms of PvE content, I think the only thing you miss out from not being in a nation is the ability to access 3 nation dungeons. I think it's only 3 anyway, going by the Hall of Fame thing in game... all the other dungeons are ind or guild, most of them are guild.
This does make Pirate harder to get though as the only way to get Davy Jones' Heart is to get it as a gift from an independant merc, or buy it off market for a ridiculous price. But then again these mercs are optional i guess.
Wonder if NDoors KR will fix the KJ system... It really, really shouldn't exist. There are already so many options for players to PvP consensually, and the open war system. KJ has no value.