I don't see Eugene, Abraham or their mission as the main plot to the story. IMO, Rick and his group is always the main story line. The show and story has always centered around Rick and his crew, and there have been many, many, side plots that entwine and create a great overall story.
So where was Rick and his crew headed after Terminus? What was their overall goal? What was the direction the show was headed after they escaped?
The answer is they had decided to go to DC, and the idea of a cure and an end to the apocalypse seemed like the best direction to go. They finally had a reason to get up each day and push forward, other than just to live to see the next day. Granted, it didn't get very far before it was derailed, but now aside from the side plots, there is no longer a main plot, a main goal for Rick and his crew. They are back to where they were right after the prison was compromised - nowhere to go, no hope of ever being safe, and no long term plans whatsoever, other than to just survive.
At some point, you need a main overall mission or story to keep a series like this going. Surviving for the sake of not being dead is not much of a story. Even the characters in "The Road" had a goal, a reason to get up each day and move forward. There has to be a "light at the end of the tunnel".
Personally, it is that light that makes the Post Apocalyptic genre so appealing to me. The survival, gathering of people, formation of a society of some sort, the goal of finding a place to call home and defend, and the rebuilding of humanity. If the intention is to just roam and survive with no end goal in mind, there just isn't much point to it all. There has to be a higher reason for me, a reason to tune in and watch the drama of trying to get from point A to point B, and being on the edge of my seat waiting to find out if they are going to make it to point B and get one step closer to their goal. Plus, if they don't have a goal at the end, what makes them different from the group Daryl was with last season?
I look at shows like "Falling Skies" and "Revolution". The first seasons of each were awesome because there was a story and an end goal. Falling skies made it two seasons before the main story line hit a brick wall, Revolution lost it's main story line after season one and died a slow death. I tried to watch season 4 of Falling skies but it was so convoluted and unfocused that I just had no desire. I couldn't make it 5 minutes before I was asleep from boredom. Half the reason I am excited for the next 3 episodes of Walking Dead is to find out "what is the new plan".
The irony is, the closer they get to accomplishing their "end goal", the closer the series is to ending. If the prison had worked out and they had finished clearing it, built better walls, and lived happily ever after, it would have been a lame show, and it was headed that way until they brought the governor back. Even the sickness in the prison was just a weak mini-plot.
Imagine the despair you would feel in a situation like that. Unless your idea of a good life is being a marauder who just runs around preying on the weak and taking what you want by force, you would need a reason to get out of bed each morning, to keep fighting for survival. But they touched on it last episode: at this point the only ones left are the strong people. The rest are gone. And Abraham was ready to check out until he had a reason to keep going. Matter of fact, suicide was very prominent in the first 3 seasons. A lot of people just figured "what is the point". And that is the big question now.. what IS the point?