Normally second person (writing from the reader's perspective) works well with deeper writing. It helps connect the reader to the story, and combined with lush detail and strong emotions can make a fic really stick out. However, it usually works best with short works such as oneshots. Going through a whole long chaptered fic that places you directly in it, rather than a regular character, can easily get boring and repetitive after a while.
It really depends on the context of your story, though. You have to keep in mind that you can't just make any plot for a fic and stuff the word "you" in it all over the place. Think of it this way: Would the story work with relatively the same effect if you'd used a normal, first or third person character? If so, it's probably best to not use second person. It's rather awkward to show long-term character development and plotty events while dragging the reader along in the story, especially when you could give the same effect without this writing style.
That said, second person goes best in short, deep bursts, making it perfect for some oneshots, but very hard to pull off with most chaptered fics. I'm sure it's possible to pull it off, though, without it seeming too awkward. You just need a very creative means of writing it, and an actual purpose to using second person rather than either of the other POVs.