I'm thinking about cutting the amount of techs and buildings down a lot. Remove everything that doesn't do something. I think a handful of techs is enough in every category - about 20-30 in total. Additionally, not more than 10 buildings. Keep it really simple. Everything should have a non-subtle positive effect. I realize, the game will be very easy to play this way, but that's OK. Penalties can be introduced later.
IIRC, everything that's currently in the tech tree does do something, with the exception of theories. Of course, there are things that are a bit extraneous, like distinctions between different weapon types that don't really affect gameplay right now, and stuff like that. The ships tree, for example. could be simplified greatly to include a simple progression of 2 or 3 each of SR weapons, shields, ship hulls, and stealth and detection technology, with a few techs for planetary shield and defense, (perhaps a single tech that increases both). Similar things could presumably be done to compress the other trees.
Though to be honest, I'm not sure of the need for that (except that some pruning of the ship tree probably would improve playability). It's unlikely to be a move towards the game's finished state, and as it is now, there are enough techs, all of which actually do something, to keep the player occupied for a fairly long game, which I think is probably a good thing. Additionally, the structure of each category is quite simple, and there aren't a lot of complex interdependencies.
The biggest problem with the tech tree IMHO is the large amount of theories, i.e. techs that don't do anything but lead to other techs. The ship branch does seem rather large.
The biggest problem with the concept of FO's tech tree, IMO, is theories, period. I'm currently working on a tech tree that doesn't do anything to express several ideas about the tech tree structure, as well as brainstorming about future additions to FO, but that has very little bearing on current playability...
Glancing through, a lot of theories could be combined with their most basic application. Having the occasional pure science theory is fine, but currently the tech tree is nearly half theory. That IMHO is too many techs that don't do anything.
I think I tried that once, and Geoff was all like "Nuh-uh!". But I didn't really pursue the matter, so I don't know if he would have ultimately agreed to it, or if it was really a good idea (I really don't like techs that don't actually give you anything).