Sorcerer, you said you are open to ideas few pages ago, so I'm dropping this here.
Regarding whole research system, I came with few ideas. Do not wary, I do not expect them to be used. Mainly because I do not know how much can be moded. I'm sharing those ideas to ease my mind, it was hard to fall asleep last night.
My ideas depend on some factors I'm not aware if are possible to mod or not.
1. Idea system:
A pony with high skill in related job would have a chance to come up with an idea of new use to the material he works with. Example: gem cutter of outstanding skill would at some point get an idea of growing gems in to crystals. opening new research project. This would work similarly to "mood" system. Pony with the "idea" would need to claim a library to write down basic explanation, so other ponies can start the research.
2. Expanded studding/research:
Now that we have open research project of gem growing, a research on the process has to be performed. Gem growing research would contain of smaller projects that have to be completed. So now we got: "Small volume gem growth process", respectively "medium" and "large". To perform research on small project, ponies have to use related materials, in this case gems of respectful sizes. To perform those projects ponies would use related skill, in this case gem cutting. Researching projects would yield research notes. Depending on quality of the note it would be useful or not. That way, high skill ponies would have higher chances of succeeding in research. Low quality/useless notes would be destroyed.
3. Research director:
This is the pony in charge of all projects. He would need high bookkeeping skill (because its related and can be trained). This pony would gather and combine all useful project notes in to complete projects and eventually complete research and blueprints.