We all know that the WoM research model is significantly imperfect, but an idea I just had would fix many of those problems while keeping the flavor.
In this model, every turn after a breakthrough, the game would roll randomly for each tech (which you have the prerequisites for) to determine if that tech would be added to the list of techs you can choose to take. The chance of a tech being added would increase with the amount of research being done and the number of turns spent without a breakthrough, and would be lower for more "advanced" techs. At any point, the player can choose from the tech options currently available, and obtain the tech they chose. All the other options would then be removed, and the process would start over.