Add Oil for a 'better' engine->+ movement. Add some other thing for offense and another for defense. (better weapons/better armour)
But then it always comes back to being very complicated to get anything 'properly' built.
I like the way it was done in Civ IV, where refrigeration gave + movement to ships and beelining to CS wouldn't give you macemen unless you had ironworking researched (same with infantry and rifling). I didn't find that a particularly complex idea to handle, so I'm doubtful of the benefits of streamlining.
That said, in the context of Civ V, I'd like to see some balance between the top and bottom halves of the trees. Economy and science are more desirable than military in most games I've played (heck, most of the time the goal of my military is to get an economy and science from someone else), and rightfully so - but starting with Medieval I find myself coasting along the top half of the tree for ever-increasing science and happiness rewards.
I'd like to see the tree rebalanced so paths aren't all-military or all-science. The opportunity cost of passing up the HS->GE->Education chain is pretty huge, and given all the rebuilding you have to do after a conquest, going along the warmonger path near the bottom isn't that decent if you don't have the economic techs in hand. Plus, if you look at the icons alone, the one-unit military techs give the player much less than the science techs that have building and wonder icons bursting at the seams.
I understand that the designers didn't want to tie science and military together in a positive feedback loop, where the one ahead in tech is also the one ahead in military - but the science techs themselves too closely tied to economic techs which create a positive feedback loop for the economy. I would like the techs to be decoupled and the buildings and units sprinkled around the tree, so that instead of going for ideological purity a player can mix and match what he needs.
For example, get rid of Physics and move the Trebuchet up to Machinery to make the tech compete with Education. If the top half is going to be really science-heavy, then make the lower half have fewer techs so the two paths can compete. Make the University have only one specialist slot, with one more opening up after Scientific Theory to showcase the effect of the Enlightenment on the elites. Since universities are (and were, historically) less important, the player would have less of an opportunity cost for taking other paths.
Move the Notre Dame to Acoustics (and rename it Aesthetics), so someone going for happiness will really have to plow through the 'filler' happy techs to get what they want, instead of getting happiness as a by-product of researching a science tech.
Move the cannon down to Metallurgy, and have it reveal Coal instead of Scientific Theory. Now production (in terms of Coal resources and pop from fertilizer) will be aligned with military units, and the science techs are aligned with science and not science+happiness+production.
I'm not familiar enough with the Industrial and Modern tech trees to make decent suggestions, but I'll take a shot at it anyway.
I tentatively suggest merging Railroad and Replaceable Parts by renaming Railroad as 'Replaceable Parts' and moving all the techable items into the new tech. It'll get rid of filler, and put rifling as a prerequisite to Infantry. The new Replaceable Parts will still lead to Flight.
Take Combustion, and make it one of the Electricity techs that also requires Replaceable Parts. Tanks will now be have Biology as a prereq and will be the unit with the most prereqs needed to research in the Industrial era, but that's not too shabby considering their historical importance.