Even after all this time, you still haven't changed even one bit, Naruto. You made friends, changed people's lives and even saved the village countless times; yet you still do it alone. Sure, we were there most of the time, but were only support. You always do the major ones, in all actuality. It wasn't fair for you.
Everytime Shikamaru saw Naruto, his first unconscious thought was always: "What is it really that you're carrying on your shoulders, Naruto?". Even though Naruto is still his idiotic self, Shikamaru can't help but think, or maybe feel, that deep inside, he's carrying a lot of problems.
It became more apparent when Naruto returned to Konoha after three years. It was as if, along with the techniques and experiences that he got from travelling with Master Jiraiya, came problems that weigh him down. The brunette shinobi doesn't know how he knows all of this, and frankly he doesn't care how, but he just knows. And it's been keeping him restless.
Along with his observations of the blond shinobi came realizations on his part. Shikamaru realized, after all this time, Naruto was shouldering the responsibilities of a lot of titles he has been holding.
As the "unproclaimed" leader of the rookie 12, he had to be the one to defeat the "major" enemies. He had to always help his friends. As Sasuke's friend, Naruto had to save Sasuke from despair. As Tsunade's chosen shinobi and Jiraiya's chosen student, he was expected to always be strong for everything.
Shikamaru belatedly realized that even though they were partially at fault for not being able to stop Sasuke, Naruto was selflessly shouldering all the blame for it. That guy really isn't fair with himself.
So, along with his realizations came a very disturbing thought that may bug Shikamaru for life; the thought that Naruto will someday fade along with the light; the light that somehow represents all of Naruto's problems.
It was a very foreboding thought. Because Naruto MAY just fade someday. He has a habit of disappearing in battle at times after all. Frankly, it scares them ALL, somewhat. That Naruto may be killed while no one's watching or something. So, it's always a relief that he comes back all the time, a bit bruised and tattered, but alive all the same.
That's why Shikamaru wants Naruto to realize that he had friends; friends who'll support him through everything. He just hopes Naruto does realize that before he, or they, fades.