By this I don't mean, my pointy stick is bigger than your pointy stick and does more damage. I mean this unit has X equipment which makes it act radically different from your man with the bigger pointy stick.
I agree with most things you posted, and particularly agree with this quote here, since it captures the essence of what I mean: NOT (only) bigger and better as options, BUT rather different, for example, in terms of combat: Stealth or fear instead of pointy stick; tactically, but not universally, useful shield wall instead of "better" armor; etc.
With synergetic cross-path researching, I mean that this would introduce a method of adding differences into the game mechanics without making each breakthrough the sole measure of a discrete changes; this might be able to increase strategic choices because it would make various options more viable for players -- in the sense that every tech tree, and many breakthrough milestones on each tech tree, become enhanced in value for every player at more stages of the game. In other words: It would help avoid the situations we know from other games (be they RPG or TBS) in which investing in a particular tree becomes meaningless once a certain set of conditions has been met, for example: (RPG) Once your character has purchased X or more "dual-wielding" skills, it becomes increasingly meaningless for that player to purchase any "archery" skills, thus narrowing a player's set of valid strategic choices; (TBS) once your city has built X or more military production buildings, building economic boosting buildings becomes increasingly meaningless. With more synergies, we can expect a player to have invested heavily in Warfare to be rewarded by having big strong armies, and his options will also still be varied, in that she might choose to invest in few squads of elite horse soldiers or large squads of decent archers; yet the players will have more "flavors" to choose from if, in addition, their research into Civilization or Diplomacy etc also add different flavors to their warfare path they can, but need not choose from, such as some I suggested (battle priests, spies, etc.) -- not just pointier sticks. This would also reduce the chances that all players continuously beeline for one particular path to master because this is the "best" option.
Additionally, this would also increase the net amount of variations possible in-game, and thus make late-game combinations less foreseeable; for example, some particularly elite abilities I suggested earlier
e.g.1: breakthrough Advanced Charming II (Magic path): lets you cast a hard-to-resist combat charm spell called Compulsion on most Kingdom humans, a high-level breakthrough, as well as a non-combat charm spell Conviction used only on envoys in friendly cities; but if you ALSO have Subtle Talking II (a mid- to high-level Diplomacy breakthrough, which itself gives you the ability to negotiate MPPs with neighbors at a high bonus) then the breakthrough Advanced Charming II might ALSO gain an additional effect, e.g. a substantial bonus to the spell Compulsion, and the ability to cast Conviction with a bonus as well as in all cities, not just friendly ones; but IF you ALSO have the breakthrough Advanced Animal Speech (high-level Adventure path), then you may cast Compulsion on ALL entities of all factions, including animals.
Just an example. What I am saying is that (1) during the later game, people might still be getting interesting benefits from discovering even lower-level techs from unspecialized trees often considered to be "wasted" in other late-game scenarios (thus also helping to avoid late game tedium), but also (2) later game permutations will be increasingly interesting, varied, and unlike the my-stick-is-bigger-than-your-stick foreseeabilitiy; and (3) the strategy of technology-pushing (that is: concentrating lots of resources into research) into various branches becomes viable for rare multi-path possibilities that not everybody will be able to obtain (e.g. abilities which require at least 3 different mid+ or high-level breakthroughs) in the course of one single game incarnation.
Moreover, it might also make for less clutter. If you want to have, say, 1,000 "abilities" in the game (actions, statistical boni, empire-wide effects, spells, building options, combat maneuvers, etc.), you might be well off having 1,000 discrete breakthroughs required to enable these, by having about 200 breakthroughs per path. But what if you want to have (or mod) 10,000 different "abilities". Attributing the ability to perform or unlock or build or activate some of these abilities not to one discrete breakthrough, but to more simultaneously, will give you (especially you as a modder) more room. That way, one early breakthrough, say Simple Mining, might give you up to 100 boni, depending on what other breakthroughs you have unlocked and what other conditions apply later in the game.
