Increase the penalty for focusing on one tech even more than it is today, this would be a simple and yet effective tool to persuade folks to level their research across each of the tech areas.  just my 2 cents...

One could perhaps put some tech prerequisites from alternate branches, especially for really powerful techs. For instance certain metal weapons might require a Mining advancement in the Civ branch, powerful magic weapons may need advancement in the war branch and some of the more powerful Civ techs could have diplomacy pre-reqs. Tech can be kept organic and still have connectivity between the branches

I don't think its as simple as that.  In a competitive multiplayer scenario, focusing on anything other than Warfare/Conquest will be a huge gamble--that your neighbor is also playing pacifist and is not going to leap at the opportunity to double his empire in size in the early game.  An early capital conquest is much more economically valuable than the improvements unlocked with the early civics tree.  There -has- to be a mechanism in place to prevent a repetitive metagame.

this. make us need magic and diplomacy to avoid being outmaneuvered, rather than hiding warfare and civics in other trees.

Has anyone here played Space Empires 5?  While the game has many flaws, there was one thing he got very right, the Tech Tree.  It was a marvelously simple idea that worked very well.  You generate Tech Points by building the structures that supply those points.  You then allocate those points as you see fit over any of Technologies available to you for research.  Generate 1000 points, you could assign 200 to engines, 100 to Photon Beams, 325 to Shields, 100 to Colonization and on and on.  Of course you could also assign all of those points to 1 tech as well.

In my opinion, it doesn't make much sense that every single Tech institute or school would all be focusing their efforts on Warfare until we reach a new level of advancement and then up decide to work on something else.  Give the player control on where all those points are being assigned to.  

 You already have the various summons letting your sovereign generate an instant army, and by level 4 you can have the kind of tough critters that need something a bit more serious than a party of club wielding peasants to take out - achievable rapidly if you have an arcane temple in your empire. Magic research gives you access to legendary plate, which lets you make a hero invulnerable to anything less than a serious attacking force or severe attack of bad luck. Then you have the adventure tree which is going to be a wildcard. Not only can you pull superior equipment from your heroes out of the higher level dungeons, but with a little luck and some magic research you can equip the elementium stuff. And from the first advance in that tree you're causing more dangerous monsters to spawn throughout the world, with the chance that any attempt at a rushed capital conquer could vanish in the wilderness before it even reaches your border. And of course without some research into civilization the conquest tree is useless. Good luck affording anything but a stick armed peasant on the 6 gold per turn income a single goldmine owning town will bring in without development.

There are several problems with that theory.  Firstly, by your own admission, it requires a high degree of fortune for optimal performance.  If you've played strategy games in competitive settings before, you know that the way to win is by employing methods that produce stable and relatively predictable results... essentially the difference between playing a game of Texas Hold 'Em vs. playing cee-low dice in the alley.  The key to success in strategic gaming hinges on your ability to accurately assess your strengths, your opponents strengths, and the general outcome of the various options available to you, and based on this knowledge, choose the best path.  This is just plain impossible with a strategy that relies on randomly generated quests and rewards.

Secondly, you completely mischaracterize the strengths of someone pursuing a Warfare/Conquest research focus.  They will not have "peasants armed with clubs" by the time you have reached LEVEL 4 spells at the minimum to get decent summons!  Even if you rushed straight through the levels without pausing to research a single lower level spell, you will be outpaced, and your opponent will be generating 8 figure troops with warhammers.  How you would even survive long enough to summon your stone giant (who, by the way, can only fire his ability once every three game turns) is beyond me.

Third, and lastly, where are you finding enough elementium to reliably supply even one multi-figure unit, let alone attempting to keep pace with someone that can crank out troops restricted only by metal.  What game are you playing that heroes are unstoppable?  I suspect the answer is "Elemental, single player, with autosave every turn and a reload every time one dies."  Heroes are weak to the point of uselessness, unless you are using the bugfix mod which enables shard spell damage multiplication as it was supposed to work at release.  Then heroes can crank out good damage if you find a shard aligned with your spheres and imbue them.

That's just a gross misrepresentation of facts and absolutely impractical given an opponent that is playing to win.

Perhaps, instead of arbitrarily limiting narrowly focused research, it just becomes more difficult by a certain % for every advancement made in a row, starting at 3.  I dunno.  But, and soon we shall be able to test, any player in a serious game that does not rush warfare will get curbstomped before turn 75.

I think that it should be feasible to go all in 1 tech branch or to spread out evenly. The key is to make it so that you can get 50% tech in every branch in the same time it takes you to max out 1 branch. Also plan it out so that you can't max out more than 2 or 3 branches before the game ends (for an average length game).

The main balance point is to make all techs equally appealing, using pro/con system.

That's forcing a style of gameplay down people's throats.  The key is to make different paths, and no path- viable.

Diplomacy, Adventure, and Magic tree issues can be solved with balancing, rare techs, and expansion.  Right now the first tech I research tends to be trading.

I haven't checked yet, but -maybe- if you are playing on the fastest game setting with a sovereign with bonus arcane research, but if you're playing on that speed setting then tech research is amped up as well.

I would also contend that even your level 4 Fire Elemental summon is essentially useless against multifigure units.  Its ranged ability is not very great, and it will die to a single hit from 4 or 8 figure warhammers.  You get more leverage out of Rokoth's Promise, but that's at LEVEL 5, rain of stones can only be cast once every three turns, and does not do enough damage to stop even four figure units.

Have you actually used those 40 defense heroes in combat without reload cheesing?  They die.  A lot.  They just don't have enough hitpoints to survive.