The train car pulled out of the station and John waved goodbye. It wasn’t tearful, it wasn’t joyous, yet it wasn’t indifferent, either. He sensed something welling up inside him, something he could not identify. It began near his chest, traveling slowly, almost imperceptibly, up towards his throat. It stopped there and hung like an anchor. It weighed him down in the tattered brown seat and, for a second, he felt he had made a mistake. But then it began to sink, the anchor being cut by some merciful fisherman trolling the water just below his chin. It moved back down, passing his heart, only lingering for a second, before settling inside the lining of his stomach. John opened his mouth softly. “Excuse me, sir?” he whispered to the conductor, tugging on his arm as he walked passed.
 

For a hook, this just seems to droningly negative. You are trying to invoke curiousity, not sympathetic depression.

It is actually unclear if John is on the train or watching the train.

", almost imperceptibly"
imperceptibly to whom?

"But it began to sink, the anchor being cut..."

Seems like I would expect a less gradual sounding reaction with the 'cut'.

How do you open your mouth softly?

For what its worth, on first read I thought it looked promising. You clearly have the talent to pursue writing. I had to look pretty closely to nitpick the things I mentioned above.
 

Does this work any better? Or does that amount to a pointless shuffling of words?
 

When you do rewrite it, look at what everyone said and think about it for a while before typing out the new words.

Read carefully over what people say and decide for yourself whether they are right and if you need help understanding what to change, ask for clarification.
 

I would work on cutting away some of the internal exposition. While you've set a wonderful tone and use some excellent imagery, it still feels like a little much to be hit with right of the bat. My suggestion would be to shorten it up to get to the "why" of his emotions. Who has he left? What kind of mistake has he possibly made and if it is a mistake then why is leaving? Answering these questions will go along way in establishing conflict and keeping the reader involved. You don't have to give it to the reader all at once, but give the reader something that shows motivation behind the character's actions/emotions.

Also, for what it's worth, I also agree with pantros, you've got what it takes. Now you're in the same boat as the rest of us...you have to take on the arduous task of refining and polishing and refining again and again...and again.

I don't think that you've got too much internal imagery, rather, you've left out something very important in setting up the scene. People are sensing that and feel frustrated by the internal action because they don't know the external circumstance motivating it.

I want to know to who or what John is waving goodbye. I feel that I need to know that before I can understand his feelings. Notice that you don't describe the feeling itself, you only describe its action, that it wells up inside of him until something snaps and allows it to sink back down.

I didn't have a problem with "opened his mouth softly." It implies two things, both that it took little force to open his mouth (because it hadn't dried shut or anything) and that he didn't open it past the natural repose of the flesh. It's like the term "gently parted lips" but a little less, um...amorous.