I agree with you, there. The last episode of Blue Gender just felt WAY too rushed and condensed, as if it were mant to be told over the span of at least 2 or 3 more episodes. That said, I didn't mind some of the way things ended, like how things went down on the space station orbiting Earth at the end, but I really disliked the whole part where they into that site where the blue were disappearing to, at the end, as it just lead to a scene that felt completely pointless, to me, and actually also felt kind of boring to watch, making the ending seem quite a bit underwhelming, and hurting my overall opinion on the series, by a little bit. That said, I still enjoyed most of the series before the disappointing ending.
If it were ever remade, though, I'd like to see it remade with MUCH better animation. The animation of Blue Gender just felt so bland for me, and would have ruined the series for me if I wasn't a person who doesn't put a whole lot of importance on the quality of animation of a show as long as the story is good. Thankfully Blue Gender was at least able to deliver up on that part.
Actually, I personally felt that the final arc was going fine up until the tournament came up. I also liked the actual ending of the series, in terms of where things left off in the series. As for the tournament itself, though, I didn't care for it since no other tournament arc could top the DT arc for me (even if it was from the same series, like it is in this case), but it was extremely short so it didn't do a lot to hurt the series's overall amazing quality, for me. That's why I don't really mind if YYH never gets a remake (which it never will, anyways). But, I do agree that a remake of the last arc could be a good idea, if they kept the first half of it the same, but replaced the tournament with something much more interesting, like an actual war breaking out between the Three Kings of Demon World (which is actually what I really wanted to see happen, in the first place ).