For me, an in-game research tree cheats the civ building lie we are willingly telling ourselves. But I like the sim/world building part of games like this. I shouldn't be able to know that atomic weapons are in the future somewhere and if I follow X path I get them. It's more real to me to research "warfare" and see a progressive evolution of weaponry.
In fact, I'd dig it if, while researching magic (or some such thing), something goes terribly wrong (as research does) and I hit a dead end and lose the points I spent or I get the tech but the inventor dies in a related explosion.
Good times indeed!
I really like the idea that, as a Sovereign, you are telling your little bookworks what areas of your society need to be improved on a macro level (your five tech categories) and then they come back with the micro results of their work (the actual techs).
It feels more realistic (not in a "zomg! real world sense, but in an I'm a magical king with two hundred and seven different things on my plate so I give them direction and then let them get to it sense). In fact, I'd take it a step further.
Instead of selecting your research category, waiting X amount of time, and then being presented with an array of psuedo randomly chosen technology choices I'd have the Sov. select from subcategories and then have the researchers just discover something in that category. All of prereqs and technology relations would still exist, they'd just be invisible to the player. You'd still be choosing how to specialize your society.
For example, under Civilization you may have the subcategories of farming, production, economics, and housing. You, as the Sovereign, decide that your people need to strengthen their ability to feed themselves. You tell your minions to go focus their research efforts on "Civilization-> Farming". They come back with one of the green, yellow, or red techs that would have been available for you to choose, but you never see the options. They just come back with their discovery. "Sire, we've figured out how to produce food from bees!" You just got beekeeping. You want more, you keep your focus on Civ -> Farming and they go back at it and come back with another tech under that category.
I really enjoy the idea that you can't map out your tech path to exactly what you want, but I feel like the immersion of the system is broken when, upon reaching your next research goal, you're presented with a list of choices.
"Sire, we have finished our efforts! We can have discovered Beekeeping if you like. Or Farming II. Or Economics. But only one, even though whichever you pick we'll have discovered right this second no matter which you pick. And the next time we make a discovery, you may not have Farming II again and if you do, it'll have been harder to get!"
No matter what the system ends up being though, the tech screen certainly needs more information. I don't know if there aren't tooltips yet for the little icons each tech gives you (granary, armory, etc), but I don't get anything when I mouseover. The first few times through the game, that will be frustrating for players. "Great, I can select this tech that gives me an Armory... What the hell does an Armory do for me. Hmm... can't mouseover it to get an idea."
I really like the system as is, I just think it needs to be presented to the player in a better, less "what the hell is going on here?" fashion.