See, that's what I thought too the first time I watched the movie. I liked the idea of him leaving to find himself and even though he loved her, he had to figure things out within himself first before he could start anything with her. I hated that it had such a typical, romantic ending.
But then, I saw it again a couple times, with and without the commentary, and I realized what Zach Braff was trying to get at. He wasn't trying to say that you have to find that special someone or else your life is pretty much shot to hell. He was saying that sometimes, you have to just be spontaneous and take risks. Andrew's whole life was spent following a regular, mundane lifestyle. He works at a restaurant and auditions for a couple acting jobs on the side but that's it. His life is plain and boring. Then one day, he comes back to his hometown and meets this girl who changes his whole outlook on life.
Now, he's got this schedule all worked out for him to go back home. If he
did go back, he'd just be returning to his old lifestyle where everything's safe and planned out and where he's completely indifferent and numb. Or, he could stay. Screw his job, his apartment, all those things in LA. He loves this girl and he doesn't want to risk losing her. So in the end, he realizes that (as sappy as it sounds) his home is with Sam. Zach wants to tell the audience that a lot of the time, as you grow older, you don't really know what home is anymore. You have to find that for yourself. For Andrew Largeman, home is back in New Jersey with Sam. For other people, home could represent something else.
That's why there's that montage at the end of all the crucial characters who are all just trying to find themselves. Andrew already has and now it's their turn. That's basically my interpretation of it anyway and, from some of what Zach says about the movie, I think that's how he sees it as well.
