From my understanding there were three projects setup in the late 00s. A Sequel movie trilogy. A live action movie, and a remake of the original series.
Supposedly the remake was suppose to air first, but it got technical and more detailed than whoever though the idea up originally thought. The sequel film (Yamato Resurrection) came out first in 2009 (It had been in development hell since the early 90s). This film takes place about 17 years after "Final Yamato" and has mostly a new crew. There is reportedly a "Part Two" in production.
Then the Live Action movie came out in 2010. No suggestion of a sequel to that was ever announced, nor does one seem likely.
Then in 2012 and 2013, the remake of the first series comes out. Yamato 2199 is doing fairly well so far.
And yes they will visit the Bee Planet again in Chapter 5, but the story is going to be a whole lot different. Something about ancient civilizations and subspace portals or warp gates from the tiny paragraph on the episodes.