Another alternative that I'm fond of is to have the base theory for energy shields be in the Learning category, whilst not actually making it an "Age" tech. Thus you'd have a theory in Learning called "Energy Fields", which would unlock the "Energy Shields" theory in the Ship Defences category, the "Energy Lab-coat Cleaners" theory in Learning (which would have applications in Learning) and the "Energy Field Growth Enhancement" theory in Growth.
In this system, "Age" techs would also be in Learning, but would be extra-important root-of-the-tree type techs, which form the root of a new prerequisite tree of major / general theories in Learning (the new "Age")
I favor this, personally.
Also, forgot all about the theory/application thingy when describing my techs above.
Obvioulsy, they would need to be reworked.
Heroic Exploration (Theory) [no effects, it's a theory]
--Propaganda (application, thinking of something like the US space race providing inspiration, needs a new name, same effects as Heroic Explorers.)
--Peering into Infinity (application, would be reworked to include a chance for a black hole cult arising as a special on a planet during Exodus Age)
--Monument to Exodus (application, unlocks build project of the same name)
Self-Organizing Databases (Theory) [no effects]
--System Archives (application, unlocks build project of the same name)
--Encyclopedia Exodus (application, increased effects from the description above)
Secrets of the Starlanes [theory with no effects]
--Starlane telescope thingy (application, unlocks build project of the same name)
Together Self Organizing Databases and the Starlane Secrets tech form the prerequisites for the "next Age" tech:
Age of ***** (Expansion?) (big theory)
A theory that unlocks lots of engine and colonization techs in other categories, plus the next bit of the Learning tree, plus some "extra credit" techs like "Energy Field Manipulation" that are not needed for the next age, but unlock nice toys over in the military categories.
Course, theories that primarily unlock military stuffs we can safely ignore in v.3.
The idea is that the player can either middle around in Exodus age, researching Heroic Exploration, or go straight for the next age. Most of the applications in Heroic Exploration lose their effects once Age of Expansion is researched--so it's an important choice.
concerning military techs, I suggest the v.3 tree be very very simple, since it will scrapped in v.4.
Exodus Era Ships (theory)
--Scout (starts researched)
--Colony (starts researched)
--Mark I (application)
Expansion Era Military (theory), requires "Age of Expansion"
Empire Era Ships (theory), requires "Age of Empire"
Mastery Era Ships (theory), requires "Age of Mastery"
Transended Military (theory), requires "Age of Transcendance"