I've several ideas about the type of technology research mechanism I'd like to see. First of all, I'd like to say that I like the new mechanism that Frogboy discussed in the "And now for something completely different. . . " thread. The ideas I mention here move along the same lines of thought.
1. Let's replace the idea of a technology tree with a technology web instead. That is, every technological advance is linked to several other technological advances. Researching higher levels of an existing technology gives you a percentage chance of discovering one or more of the technologies linked to it. For example, I've learned level 1 beekeeping. I continue to fund research into beekeeping to reach level 2. Reaching level 2 gives me a stat increase in the existing technology, say 5% larger hives that give 2% more twilight honey. However, reaching level 2 also gives me a percentage chance of discovering one of the linked technologies, say a 50% chance of discovering poisons, a 25% chance of discovering spiderkeeping, a 5% chance of discovering magical animal control, and a 1% chance of discovering flying. The examples of what's linked to what may not be completely logical here, but I think you get the idea. Because it's a web, the links work both ways, so if I'm an intense magic researching studying flying, learning higher levels of flight gives me a 1% chance of discovering the beekeeping technology. Each technology can be reached multiple different ways. For those of you who are Sins of a Solar Empire players, thing of it as if each potential technology were a planet and research is like influence spreading along phase lines.
2. I'd like to see research funded more like the way it's done in real life. If a government wants research done in a particular area, they set aside a certain amount of resources for research. Frequently they also create laboratories where research can take place to attract potential researchers. After you make a certain amount of money available to do research in a given field, researchers approach you with their proposals, and you decide which ones to fund. Sometimes you get the great breakthrough, sometimes you don't. In Elemental, this could work by setting aside a certain amount of resources as potential grants in a certain area of research. Conventional areas of research would require grants of money, magical areas of research would likely require both money and mana. Researchers would then periodically pop up offering to research a certain subject in that general area. If you agree, they start researching their area of interest, periodically gaining levels for you in the area they're interesting in and opening up new technologies to research as outlined as #1. You fund them as long as you want them to continue their project, and you can redirect them to start working on related technologies they've discovered.
Alternatively, these special research projects could be a separate research-quest mechanism outside of normal research for the unique, rare and situational technologies.
3. Make researchers a hero type. The channeler/sovereign would be the first researcher, choosing the first technology within the web to begin researching. If you build the buildings to attract researching heroes, they will periodically arrive and offer to start researching in exchange for funding (money or mana as in #2). As the game goes on, you can research multiple things simultaneously depending on the number of researching heroes you have. This allows you to increase the chances of discovering rare technologies by approaching them from multiple places within the research web (again, think of the SoaSE analogy of cultural influence reaching a planet). Making hero/researchers might also be interesting because it would allow you to create some interesting cost/benefit decisions for players. For instance, do you try to cripple your opponent's research efforts by killing his researching heroes? Does sneaking a spy into a city occupied by a particular researching hero give you a better chance of stealing or sabotaging a particular technology? Do you send your researching hero on a quest to obtain a magical item, face a particular monster or visit a particular resource in the hopes of opening up a new area of research (think, for example, of the way you had to capture certain things in X-Com before you could research them). The risks would be losing research time while your hero is away from her lab, or worse yet, losing the hero and not being able to pursue as many lines of research.
The ideas I've outlined above can be used together or as bits worked into a different system. It is a more complex system than the one Frogboy outlined in his post, although I think it could be managed using a system similar to the new mock-up he posted.
It would probably require a second screen that would allow the entire web to be viewable. In my opinion, all potential technologies should be viewable by the player, but the strengths of the linkages between should be hidden. Players who want an element of randomness in their technology research could select to have the strengths of the linkages between technologies subject to a certain degree of randomness (so sometimes beekeeping level 2 gives you a 1% chance of discovering flight while in another game it might give you a 5% chance). Variation would also be created by which hero researchers approached you, what their areas of research interest were, and what quests or materials you had for them to study.
I think a technology web would allow the situational, infinite and (sort of) random techs that are desired more organically than a traditional technology tree. A technology web also allows modders to link new technologies in more easily; they simple create the new tech, then assign how tightly it is linked to other existing technologies to define how it may be reached.