The basic Elements, originally called Reagents, solidified pretty quickly. The biggest change was making the Alembics a token instead of drawing them from the same pile as the elements.
You can download one of five snapshots of the rules, from the very first outline of what was required to the latest twist. All in all twenty-one different versions of the rules were playtested.
Layout and typography changed a lot over time and testing. Cards had to quickly communicate many different pieces of information but at the same time look uncluttered and preserve space for artwork and other flavor. Even the background image on the card conveys information about its class and function. Seen here are eight of the twelve different versions of Gold, showing how both the mechanics and the look of the card evolved.
Other cards stuck around for a while before finally being cut. The image of the Homonculus seemed to be intimately tied to alchemy, and it was difficult to let it go even after it became clear that it just didn't work in theme or mechanics.