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Lastly (for now): I know it's low priority, but I wish I could choose the color hierarchy for the minigame.  I love purple, but it only shows up when the game is complex enough that it's not so fun anymore.  When I finally get enough experience in the game to make it easier and more fun, the purple's gone!  I'd love to be able to set the colors in some menu, individually, either ordering the colors I've discovered so far, or specifically choosing custom colors for each difficulty level.  Also, would be kinda nice if getting a high score at the game gave you an extra potion (if you were doing at least X potions).  Say that for every four potions you're making at once, there's a chance of a fifth potion, so if you were making 12 potions, you could conceivably get back 15 (some chance of getting 13, lower chance of getting 14, very low chance of getting 15), and it's based on how well you played the game.  Also, would be neat to have a bonus round of some sort if you get the potion done and there's still X seconds left on the clock, but only when it's not the easiest level (because that would get tedious).  Maybe an option for which level is the lowest level that bonus rounds kick in on.

Actually, related to that: Have you ever played Puzzle Pirates?  The gameplay is based around a lot of different minigames.  It'd be neat if this game eventually got a couple new minigames for different aspects of gameplay.  Or gave an option of which of three types of minigames is the one you'd like to play for alchemy, so there's a bit of a switch-up and it's not quite so tedious at times.