I definitely feel that. I posted a longfic recently that I started four years ago, and in the past year as it's finally come together I've had to throw out a lot of stuff I wrote earlier, before I had a clear conception of the whole story. Things that wouldn't work because of restructuring or character decisions, or... in my case, just because I realized they weren't very good. :P I probably cut at least 5K, more if I count the parts that underwent heavy rewriting. I don't consider any of that wasted energy, though. There were pieces I was able to salvage and shape into something new that I liked a lot--and even the parts that were un-salvageable were part of the process.

I've never played Borderlands but I think it's really neat how different sci fi series can kind of play together in one's head that way. I can definitely think of a few that have influenced how I write in the RvB universe.

Good luck with those next steps. <3