The reason is simple. I was dissatisfied with the way the early chapters were handled (them being so short was but part of the problem - compared to the later chapters, the writing was abysmal), so, as I mentioned on Starfleet Jedi, I'm completely redoing the fanfic.
Another reason is that it just felt... well... incomplete, universe-wise. Some races I would've liked to use somehow were dropped, some elements were added that contradicted each other, and overall, I felt it was a mess.
The fact that I had no idea what I was doing, and thus, was making it up as I went along was just icing on the cake.
Now though? I have a much better plan of what I want to do with this, and have ideas to make it run smoother. The fact that my writing is infinitely better than it was in 2011 is simply a bonus.
So, coming soon, we'll see the FPE reboot, "Fluidus Potentia Evangelion" (first chapter already on Starfleet Jedi's forums).