I read this story in an anthology and really liked it, but can't remember the name or author. What (I think) I remember: The story centers around a young man who lives in a mining colony on Pluto and is quickly falling in love with a young woman he meets there. There is trouble brewing on Earth - something about a new and cruel government that is sending a ship to Pluto. The colony leaders decide to build three generation ships from available resources and escape in three different directions. The young couple make plans to be certain they are on a ship together...the generation ships are completed but the ship from earth surprises them by showing up early, in a panic the young man gets on a ship without a thought for his girl friend and escapes without her...
I won't describe more, but in the end it takes him ten thousand years to finally cope with the remorse he feels about what happened.
Edit: I believe I read it within the last three years or so, but have no idea how old the anthology was that I read it in - my impression from memory is that it might have been just as recent.
To describe more of the story - He becomes one of the circle of leaders on the ship. They (the leaders) take a drug that makes them essentially immortal. The idea being that they will be the memory to keep the future generations on the ship from drifting from their goal of escape to a new world. If I remember, the estimated travel time was tens of thousands of years. The leaders DO end up aging, but they slowly (over thousands of years) use technology to embed themselves into the ship. I'm not explaining that quite right...they create life supports and interfaces with the ship to keep themselves alive. The main character - who ends up being the last of the initial escapees remaining alive - over time becomes less and less interested in the generations on the ship, and becomes more introspective and extro(?)spective, and more and more a part of the ship. In the end the ship is intercepted by another (friendly) ship from earth. A case of technology advancing past the initial state at launch. The people on the new ship offer to take away the 'beings' on the generation ship and leave the main character to his thoughts. They are no longer really human, as ten thousand years have passed, enough time for the species to change entirely - the generational travelers have devolved, and he has basically merged with the ship.
Edit - 2
I'm not sure how to handle spoilers, so I meant won't, but not in a confrontational way!!