@Sunflower After looking your notes I went back and had a retry of the game. The issue was that when I was playing it I wasn't really thinking of the puzzle-- My computer's been acting up rather badly for the last three months-- and missed the fact that there was a viable replacement after I picked up the third Graph. I ended up completing it. My only gripe is that it would have been nice to pick up something that could allow transport to Graph Theory, I'll admit I got lost trying to find my way back once I got to the point that I was changing most of the map after each visit. Or perhaps some sort of 'map' that you could carry.
As for my game? You asked about Aisling and Ashley? Well I'm of several minds in regards to it. On the one hand, I see them as two separate people that are connected in space/time for some reason, who have to share a part of their mind with the other for some reason. Another thought is that it's all happening within one person mind, with Aisling being the more childish/full of wonder and imagination side and Ashley the more adult and serious side, and something caused a sort of schism in the person's mind. Another thought, perhaps an explanation for the previous one, is something like a 'Coma Dream' where her mind has created a sort of playground for her, one that will never end, and the Aisling represents the portion that wants to stay in the coma and Ashley is more of one who wishes to escape.
Either way, the Crystals and the Amethyst Shade were supposed to get more play time to explore the some of these ideas. However, I was attempting to explore as many different puzzles as I could and due to how I set up the world building-- Each of the levels was designed on a white board with me typing in each vertex manually-- I didn't have time to actually explore the story future.
The color issue? Well, I created the menus/skins coloring-- And wrote a lot of the menu code-- prior to deciding on the actual style/coloration and didn't go back to fix it. With the style/coloring of the game itself I sort of settled on it between Red and Blue are distinct colors and allowed me to us purple, a somewhat sinister colour at times, for the 'connected' portion, and use Cyan and Magenta as colors for the objects within those worlds. The coins were something I wanted to have, but I hadn't decided on the coloring style when I added them and forgot to fix them. If I re-explore it I'll likely use sprites of some sort, with something like an 'aura' to indicate the Purple items and a stylized representation of the 'swapped out' world.
Whew. (I included the answers about my game here 'cause I wasn't sure whether you'd check back for a response. xD)