Version 2.1 reworks the game's storyline so that it's no longer a kid irresponsibly being sent to defeat a generic bad guy like in Version 1, but instead it seems the developers realized it felt kind of silly so it's made clear the kid (now visibly older too in a more animesque inspired cutscene style) willingly participated in the adventure because the antagonist is a former student friend in the same military academy he goes to (so the kid has experience regarding what he's sent to do) who wanted to be respected and the protagonist wanted to reason with, so there's more personal stakes at play.

The game got (justifiably) easier too, normal mode allows you to take three hits and noticeably a lot of enemies have less abrasive and trollish attacks and some even have more of a telegraph to react from instead of basing everything on a guessing game. However, making it easier sometimes comes at a cost of simplyfing an already straightforward world to explore, namely now the kid can breath underwater forever, so at least two sections of level design had to be removed because they wouldn't make sense in regard to its puzzles.