John Watson knew he came second. To the thrill of the chase, to the connecting of clues, to the brilliancy of deduction. To the work.
And he was fine with it. Really he was. He was content to follow the lanky detective's lead. At first, John thought that maybe it was some kind of absurd Stockholm Syndrome (ha more like Stockholmes Syndrome, John mentally joked). As time progressed, however, John realized he genuinely enjoyed it. Granted, he didn't enjoy every aspect of life with Sherlock (he could do without the thumbs in the crisper, for example), but on the whole, John liked having a purpose. He liked being needed.
One might argue that Sherlock Holmes didn't need anybody, that he was the exception to "no man is an island". This assumption, according to John, would be wrong. John was a moral compass, a doctor, a friend, and – on occasion – a stand-in for the skull. Sherlock might not need John in a typical capacity, but he needed him nonetheless.
John also knew to be careful. Sherlock Holmes was a frenzied whirlwind of mania and intellect, making it easy to lose yourself in the chaos. John knew he was needed, but he was not a doormat, and he made damn sure that Sherlock knew the difference.
In short, it was all about balance.