In short recurring theme of all kinds of corruption and SH showing better moral values even though they are the pirates.
Naruto's world is smaller and deals with different issues.People are looking for better communication and relatively peaceful life after constant fights and wars. It also shadows our own conflict of among different countries by and large.So I won't say it's about loneliness only though I don't see anything wrong with that.
Loneliness arose from discrimination and hate and it's a big deal. You are lucky if you never had to see it. Naruto and Sasuke's have had their share of it due to their circumstances but even their was a difference.
In case of Sasuke he had everythign and lost them in one night. Naruto's progressed was getting blocked due to it since day 1. People didn't want to him grow at all and question even his admission in the acedemy. The story is about his progress from having no one to even play with him people following him. But you should have noticed that current when you started reading it.
Obito is having problems accepting the harsh reality of life and wars and moving on. He wants to trap himself and everyone in a fake dream world where he can live his fantasy.
Gato, Oro, Nagato, Zabuza , Kabuto, Itachi, Danzou all have had their own reasons for their actions and they are not based on loneliness either. I am too lazy to make a list nor I remember them all. But there is greed ( Gato, mizuki), there is ambition, (Oro, Danzou), Pacifist( hiruzen) there is jealously(Danzou), there is misguided idea of justice ( Nagato), Hidan ( fanatic killer without remorse), Raikages underhanded dealings ( attempted kidnapping of Kushina and Hinata) there is Kabuto talents but trying to be someone he isn't..loyality - sometimes due to gratitude at others due to sense of duty.There is ample of manipulation, dirty politics as well. Only thing is that in Naruto it's not often that loud but more subtle.
Unlike Luffy, Naruto didn't grow up with a longing for adventure. Luffy's circumstances were totally different. Why would they be looking for the same thing? If Naruto didn't had it's own appeal you wouldn't be even wasting time posting on it.
The problem arises when people somehow expect same treatment for different plots.
Edit: Out for the night. It's nearly 1 AM here and Sunday already. Play nice and do not start flame wars.