After posting various threads about if Ninja would be locked behind the main story quest, and reading/writing on the pros and cons of both, it seems we have an answer:
http://na.finalfantasyxiv.com/lodest...dce5fa6bcb9567

Seems the rogue quests go up to level 30, just like normal, and the NIN quests take over after that up until level 50. So, it seems the rogue and ninja will operate the exact same as every other class/job combo. Is anyone disappointed with this, or are you happy it is available to everyone including new players? Personally it doesn't matter to me much but I'm glad the game is very inclusive of new players ^^