Speaking of skills specifically, those really need an open trading system all their own. Trading scrolls is by far the worst aspect of the current stores. Currently, if someone who researched something doesn't bother to make scrolls and put them up for sale, you have little choice but to research it yourself.
Perhaps one option would be that the research table itself could act like a specialty store just for skills. Prior to beginning a research project, the researcher must set a value and list of items they'd accept as payment (like you suggested for stores). Then, any player can walk up to the research table and buy the skill. And it would also show you where else in the world you can buy every skill (if anywhere).