Necro'ed, because it's a cool topic, even if it veered off course.
Civilization (the game) sort of took the right thing with what they wanted to do. With Civ, research progress was linear.. you'd always want to put 100% research into one thing, and that's why you could only research one thing at a time.
I think one thing that everyone's missing about research is that it takes time to get there. With most games, you could just say, toss 40% research in guns, 20% in physics, 40% in ethics. Then suddenly, someone declares war on you. Your guns is at 91% completion and setting guns to 100% lets you unlock bigger guns.
Well, it doesn't work that way IRL.. because there's only so much you can allocate. Guns need weapon engineers to work.. you can't just turn a bunch of philosophers into weapon engineers in one turn. And even then, giving them a whole lot of money doesn't make a difference.
Also, my experience in RL research had this one project given a hell lot more money than it needed. Well, the child psychologists decided that the children needed microwaves for the nursery, and state-of-the-art computers for the researchers, so they spent the research budget on that. In other words, the excess money went to waste.
So, I'd say, maybe one way to do it is to give all research some inertia - takes a while for research to pick up speed, and a while for it to slow, but the research rate drops rapidly once you drop funding. And make it sort of a non-linear thing, so that even if someone spends double as much on it, they don't get double the research results.