"Klingon scientists gets no respect" is implicitely in 4X, such as the penalty in Endless Space 'Space cadets'. When you conquer a city you don't typically kill all of the universitie's professors and replace them with those of you own culture/race. They won't be happy to serve you at first, and so it's expected that there is an assimilation process. I do like that in EU4 military tradition was something you built up through war experience, rather than just an immediate bonus because your culture is inherently better at war. The university system is itself a tradition that takes time to build up. I think it would be interesting if there were stats which represented which values were accepted in your culture, such as venerating science, and perhaps late game propaganda would allow you to spend money to increase those values.

I am most interested to see how Amplitude addresses this issue, because this is such a huge issue for all 4x games, and it is a thin line to tread.  The difference between making conquest the only way of winning, and making conquest a painful slog is very small.

In my opinion, it can be addressed a number of ways.

Steep assimilation requirements tied to culture would be one way of slowing conquest blobbers.  The conqueror would have to keep a sizable garrison in the city to keep order will an assimilation process happens.  If the conquered is a larger power, then possibly one could have a production queue for "sending resistance aid", spending production to slow an assimilation rate.  If the conquerer ignores the happiness/assimilation debuff, i.e. moving the conquering army away, or not leaving a large enough garrison, then the conquered get the ability to attempt to "retake" the city by means of a spawned army or something.

Or possibly something related to culture relations, ethics relations, or diplomatic relations.  For instance, if you are a scientific civ conquering another scientific civ, then the unhappiness malus to being conquered is less, or if you conquered a civ that has an extremely low diplomatic relations value with you, there is an increased unhappiness malus.

Or even more weirdly/experimentally, one way to limit the unhappiness malus would be to improve the quality of life in the city.  For instance, building better infrastructure/improving the conquered civilians way of life could, in the words of Gul Dukat, "Show them that they were wrong to oppose you in the first place. To force them to acknowledge your greatness."

All of these would slow down a purely militaristic civ.  Either they have to spend more time building improvements or keeping unhappiness in line, or at least planning their invasion carefully.

Normally, military victories are slowed down by the following natural mechanics :

- A warmonger player tends to be hated and assaulted by other AIs.

- Having a large empire is difficult to defend all of its territory.

- The newly conquered cities need time to be productives (assimilation mechanism specific to Endless Legend).

So normally it will be fine.

I remind you that the 4X are and above all are war games, and I remind you that War has historically resolved more conflicts than culture. So the fact that aggressive players are rewarded if they are good is positive.

Well, we know that in this game that while a few medals/stars can be earned through conquest, most of them require other things in order to accomplish this. Even if you do get 6/7 stars from battles and expansion, that just means how much you have to fight in the next era in order to get those same stars becomes much greater, so the marginal benefits become less and less the more battling you do. Meanwhile, if your neighbor has been peaceful but has at least fortified their home then when you attack them even if each side kills the same number of units and you take several territories they'll have actually gathered more stars and thus more fame than you did because they need to kill fewer units to earn them. While early game this might make sense because it lets you snowball your production, science, wealth, etc. it's still a risk that becomes even moreso as the game goes on.

To be fair, this is a problem that every 4x game has really struggled with. Very, very difficult to get right. The line is so fine and difficult to tread that games usually end up falling either on the "all war" or "all peace" side of the equation, neither of which are desirable.

Fundamentally, I think there's two main approaches you could take. One is to make war itself more difficult, and the other is to have penalties to expansion that balance out the effects of successful war. While most 4X games that have tried to tackle this problem have used a combination of the two, I would say Civ V and VI erred more on the former, and a game like EL more on the latter.

Personally, I massively favour the second option. Civ V has fairly significant penalties to expansion, but it mainly tried to fix Civ IV's horrific warmongering by just making war quite difficult to engage in. Cities have big health bars, good defensive damage and powerful bombard attacks. Units can't move into rough terrain and attack on the same turn, making them easy prey for the defender's ranged units. And generally, the one-unit-per-tile system slows down war dramatically, giving the defender time to prepare and build more units. The result is a tedious, drawn-out slog where each player has to issue small, micro-ey commands to a million units every single turn. It's not fun at all and it's by far the thing I like least about the game.

On the other hand, in Endless Legend (and as a disclaimer, I've played a lot less of the game than I have Civ games, but this is how it seemed from what I have played) the superior power in a war will generally take victory with comparative ease. The war is fast, fun, and decisive, the way it should be; however, the warmonger has to be extremely careful that they will not massively overextend their empire in the process, crushing their happiness and ruining the output of all their cities. To me, THIS is how you balance war. Make the war fun and quick, but make the penalties come once the war is over.

Another thing I should say is the problem must not be solved through diplomacy alone because this does nothing for multiplayer, where the "war question" can be at its most severe. 

So, combining both points, imagine you're playing a 6-player game. Your 2 nearest neighbours are very strong players, and the players on the other side of the map are weaker. You don't think you'll win through early aggression against these stronger players so you play a more peaceful sim-city strategy. You play this strategy very effectively, but one of the other good players kills the 2 weaker players with ease, takes all their land and is able to massively out-compete you throughout the remainder of the game, due to an advantage they had access to that you didn't. Issues like this occur as a matter of routine in multiplayer 4x games and the solution, in my opinion, is to focus on balancing the benefits of war, rather than the difficulty of war or the diplomatic repurcussions.

The balance between war and peace will always be a struggle in 4X games but there are some possible paths to mitigation. 

Espionage and sabotage options through a spy system, if capable of providing substantial penalties to the enemy or bonuses to owner can be a great balancing feature. This can be provided through allowing espionage bonuses to stack through peaceful diplomatic relations or actions which is then penalized more heavily if your spy is caught and it's revealed you've been undermining peace through subterfuge. 

Advanced military research is a good balancing factor if the advanced technologies are good force multipliers or provide substantial advantages. In this way, a 'peaceful' faction surrounded by more militant factions can balance the scales by having more powerful units even if they have less of them because they don't have the production powerhouse of a vast empire. Alternatively, highly advanced defensive technologies making attacking a peaceful faction a lot harder is another way to balance the engagement. 

It comes down to the decisions made by the player. A player pursuing a more peaceful game progression (by choice or by necessity) will have to balance military research with other research if they suspect they will fall under attack. You can choose to forego all defense and fast track a win condition if you want but that comes at the risk of an opponent probing your defenses and finding them lacking.