i think that if tpt is becoming to realistic most poeple don't want to play anymore because it would become to complex and less fun. the point of tpt is more to create fun things etc, instead of creating very complex scientific reactions without them understanding it.
Funnily enough my team and I have been planning and implementing a mod roughly around the lines of what you are describing. It will include most to all of the elements from the Periodic Table, and include a variety of compounds.
The main idea is that compounds are unavailable until you create them using the basic elements. This is going to be our biggest expansion to The Powder Toy and will become our first release of a fully functioning mod.
If anyone has any other ideas I could implement into this mod, I would love to hear them!