Well communicating permadeath could be more clear. In other roguelites such as Noita you die, you get a big game over screen, you get the screen showing your run's stats and your personal records, and then you explicitly get a 'new game' option which takes you to difficulty selection. In Alchemickal you get a stats screen but I didn't think it was clearly a game over screen, and a 'retry' button which implies to me that you're just respawning in the same run.
I'm not sure about the time slowdown. If you don't engage with the alchemy the time slowdown isn't really needed as the enemies that I encountered are all ranged and telegraph their shots for a long time. Maybe have fewer elements to deal with earlier on? The tutorial introduces them one by one maybe the game should too? Or should they be randomly found and unlocked which influences your choices for what to buy from the big booba lady or whatever other sources of items are in the game.
Or maybe make the alchemical stuff a passive build that you tinker with during quiet times and use the right-click controls to add more twinstick combat mechanics and powers since the player will have more mental bandwidth to focus on combat if they're not trying to pick different elemental damage types on the fly. In Noita for example I only have to think about my wand build when I'm between levels, during combat I don't have to slow time and hastily rebuild my wand to get a bit more damage against some of the enemies on screen, just point, shoot and dodge
Also just a thought if your central mechanic revolves around colour matching that's going to make the game inaccessible for colourblind people which, it's like 1/12 people it's not a lot but also not insignificant