I'm somewhat in agreement here. Many of my games have been dictated by the technology choices I made. Many of a NEW player's initial reactions to the game are based on the techs they did (or didn't) bother to research.
I agree that it doesn't lend much to players specializing their faction according to research: you need virtually everything, except select parts of Adventuring and Diplomacy. The AI specializes its research, but that just leads to grossly over-effective (or crippled, in the case of not doing Empire research) AI in one area or another.
Cross-dependency is a BIG one, I think. Some higher level techs should have prereqs outside the tree itself. This is already a fundamental problem in the game as far as balance goes for equipment. You don't need the heavy duty armor and weapons to unlock their more powerful counter parts through the spellcasting tree. While the other weapons may be more affordable, it doesn't make logical or fun sense that you can bypass two entire grades of armor and weapons, in a tree that basically says "you learned how to make weapons and armor magic." Arcane weapons and armor should require the previous techs from the conquest/warfare tree.
Part of our issues, I think, has to do with the research rebalancing. It's just a lot slower now, to start, which makes getting all Lvl 2 techs by turn 200 or whatever seem a little unbalanced.