I'm gonna throw something out here just for the heck of it to see if it's at all helpful in any way. Apologies if it's not. :)
There's an extremely well-made game out there called Sid Meier's Civilization 4, which has a rather unprecendented level of mod-abiltiy to it for a major and still-current title (all gameplay-related C++ source released as an SDK, a fully moddable Python layer on top of that mostly for UI stuff, and a fully moddable XML layer on top of that for all the stuff XML is good for). I wound up sinking a lot of time into my own big mod for it over the last year, and part of that included a tech tree revamp.
The vanilla Civ4 tree had major issues. Lots of empty space in the grid, lots of long connection lines, and tech placements and progressions that didn't even make any sense in some cases. BUT, the basic structure was fantastic, and that's what I'm getting to with this post.
Take a look at this composite jpg I put together from 5 or so separate in-game screenshots for showing off my revamped tree without ppl having to download my mod. Sorry about the low graphics quality; best I could do and still keep the filesize reasonable.
The way it works, which is what I thought you guys might be interested in for FO purposes, is the white connecting lines are basically OR requirements. Additional tech icons appearing in the top right corner of a tech box indicate auxiliary AND requirements (and have a mouseover in-game naming the icon if you don't happen to instantly recognize it).
The purple text at the top was added later (ie not from in-game) to illustrate the chronological meaning I'd given columns and tech placements and you can pretty much ignore that I guess.
But basically I've found the "OR reqs with arrows plus AND reqs with corner icons" design works wonderfully from the player's perspective, and can support an essentially depthy tree with plenty of branches and interdependencies just about perfectly.