Okay, that's pretty nifty.  Numbers we're of course going to have to chew on some more, but that's just iterative design.  Lets play with the "grow by doing" research mechanics you've put forward:

War:

Wars are hard to discretize (break up into chunks) IMO, especially when multiplayer is involved.  Instead, sum the value of all units you have killed and apply some maths to that number to get a reasonable research bonus.  If that seems too powerful, then subtract the value of your units that have died.  Or, just have the value of the bonus decay with time! Throne of Skulls anyone?  Personally, I like mine at least 3 stories tall.

Civil:

Hard to balance the turns of peace, since a warlike country could declare "phoney" war on you to decline you your bonus.  I think it needs something different.  I'll throw out a nowhere near final value: number of cities (rank 4+ settlements).

Diplomacy:

This is awesome. I do you one better.  +1 research for every treaty you have active.  So signing with a diplomatic power, you both get treaty benefits, but the diplo faction gains more.  This may be amazingly overpowered, but once again, I think its a number thing, the core idea though, is what I mentioned.

Others (Magic & Adventuring):

Magic -  you cast spells, perhaps like the War academy except number of spell points expended with decay over time, so that an empire that casts spells early and often will build a research bonus, but will be constantly depleting their spell-point-pool...

Adventuring - Lairs Explored, Heroes Recruited? All of these are possible, lets talk about them.

For the War side of things when he said wars I think he was referring to individual battles... (I could be wrong though)

Great ideas btw... I don't really have much to add, like you said it would come down to numbers, Obviously though bonuses would have to cap at some point maybe at +10.

For the Civil one I don't like the idea of it being based on cities... Could you code it so that you retain the bonus unless *YOU* declare war. That would solve the problem of other players playin cheap and robbin you of your bonus, as long as you play strictly defensively.

Everything else sounds pretty solid.

This is almost certainly possible - in fact, I like it better than the off-hand I threw out.  See, you do have something to contribute .  Yeah, caps would probably be something to consider, but if this goes in I'd want to see folk try and break it in beta with no caps first.

Diplomatic Academy

• +3 research
• +2 research, for every ally you have now (if researching Diplomacy tech)
• +1 research, for every war you have ended in a diplomacy screen (if researching Diplomacy tech)
• -1 research, for every war you have started (if researching Diplomacy tech)
  
• +1 research for every non-ally you have an agreement/ treaty with (if researching Diplomacy tech)
• +3 skill for any diplomats trained here(?)

Scholars Academy (generic)

• +4 research
• +1 research, for each empire you are trading with
• +5 research, if your empire is the least technologically advanced in the world and you have contact with at least one nation more advanced than you
• +1 research for every research producing unit stationed in the city (scholars)

Adventurer's Guild

• +2 research
• +2 research for each legendary monster you've slain
• +1 research for each legendary artifact you own
• +1 research for (1x quests completed/5)
• each time you complete a quest, adds +10 research for that turn only. Adds less research for weaker quests, and more for complex quests, always a one time bonus.
• Increased chance for rare artifacts to show up in the city's shop
• adds additional Champion training for costs of Gold (only so many trainings for each Champ?)

I like this idea.

War Academy

• +3 research
• + 5 research (if researching Warfare)
• + (1 * Net battles won) research (if researching Warfare)
• + (1 * enemy soldiers killed/ your own soldiers killed) research (if researching Warfare)
• +1 research for each Military building present (if researching Warfare)
• -50% troop training time

Library of the Arcane

• +3 research
• +4 research (if researching Magic)
• +1 research for each spell learned (if researching Magic)
• +(8 + Intelligence/ 4) research if Sovereign is present (if researching Magic)
• all magical buildings in city produce +1 spell points (cumulative)

Civil Service Academy

• +3 research
• +4 research (if researching Civics techs)
• +2 research (if researching Diplomacy techs)
• +1 research for every 20 turns you have not declared war, attacked an opponents settlement, or lost a city via conquest (if researching civics or diplomacy)
• -40% maintenance

Majestic Royal Academy

• +3 research
• +(3 + Charisma/2) research if Sovereign is present in city (if researching Civics or Diplomacy)
• +2 research for every family member present in city (if researching Civics or Diplomacy)
• +4 gold
• +1 gold and research for every level 5 settlement (foreign or domestic) connected by caravan by ONE degree (meaning a direct "friend" not a "friend of a friend")
• +1 prestige for each government building (palace, town hall)

Merchants Academy

• +2 research
  
• +1 gold for every caravan that arrives from a domestic city
• +3 gold for every caravan that arrives from a foreign city
• +1 gold for every gold producing building
• +1 research for every trade treaty
• +1 research for every foreign trade route (in city)
• items in the shop are cheaper

Academy of the People

• +3 research
• +(1 * population/ 100) research (if researching Civics tech)
• +1 prestige * city level
• -(1 * soldiers in city/ (population/10)) research (if researching Civics tech)
• +1 research for non-royal champions already producing research staying in the city

Great ideas here, let the devs consider these ideas!