Well, at one point I had investigated modding the ideologies. Other priorities became more pressing, and, I got frustrated that I couldn't change the NAMES of the ideologies in the graphics/etc. Which I know is somewhat vain, but people would constantly bicker at me if I setup a different ideology, and it still was labeled benevolence at the top of the screen lol.
My plan, bearing in mind that I can't change everything I want... was to ensure that...
1) replace benevolence, pragmatism, and malevolence, with: Unity, Consumption, and Supremacy. These align somewhat, with the existing lines, but take out the idea of there being a universal "good" and "evil" which is especially silly in a galaxy of multiple species who would naturally have different outlooks on these complicated issues.
Unit/Harmony (still pondering the name) would be about coexistence with other races and the environment: they would gain planet, morale, diplomacy, and some influence bonuses. Consumption/Greed gets influence, monetary, extra mining, some military. Supremacy, gets military, planet resistance, production bonuses.
2) The big thing here though, and the part I think you would appreciate, is that every perk, while not necessarily altering playstyle significantly, would also come with a negative modifier. The Supremacy tree, will have numerous diplomacy penalties, basically, if you pursue a course of military and genetic/cybernetic supremacy over all your neighbors and the environment, they are going to be offput by you, even if they themselves are ALSO supremacy players. Subsequently, a Unity player can pretty easily sway anyone to their side, even a Supremacy player, because they are naturally cooperative, they simply convince the supremacy player that he is getting the better deal, when reality he isn't. The consumption player will earn lots of money, be able to get more resources, and have an insidious influence (think Coca Cola and McDonalds circa 1950s to 1980s), but suffer larger and larger morale issues to their planets as they continue down the tree. The Unit player, suffers from production and military penalties, as their citizenry devalue the idea of conquering other worlds and constantly seeking a harmonious approach with their environment.
Now I'd love to change other mechanics, because as you say, some of these should be mutually exclusive, which is why I would prefer one tree for each overall "chain" with three ideology choices and you have to pick one, but I wouldn't lock you from taking a different ideology choice on the next choice.
For example, each ideology has 5 chains (I think, I might be wrong here). I would arrange the five to be universal to all ideologies, say:
1) Planets 2) Infrastructure 3) Relationships 4) Governance 5) Culture
Level 1) Choose!
A Extra tile
B Extra Colony Ship
C Extra production
Level 2) Choose!
See? So basically, while your overall ideology isn't defined strictly, you get SOME mutual exclusivity, by making a choice for each perk level. You could go all one ideology on Planets, a mix on Infrastructure, all another on Relationships, etc. This way, while you personally might not think the race makes sense, at least you know the other player couldn't have ALL cake and eat it all too! Because your right, issue by issue, you shouldn't be able to say "well my people both believe in letting people choose their jobs, but also in enslaving all life".
But I think its fair that an alien species would have somewhat radical views that may be jarring between these categories. "Yes people choose their jobs, we should live in harmony with nature, but those other aliens? KILL THEM, KILL THEM ALL!"
Stardock's current system was meant to create exclusivity in a loose manner by limiting how much ideology points and such you could get, but it completely relies on colonies/planets and in larger galaxies it becomes somewhat silly. Ultimately, they prioritized maximum player freedom, and I agree, it weakens the overall experience for more thoughtful players.
I think the above system is enough of a compromise to greatly improve the game even with benevolence, malevolence pragmatism, it also isn't a dramatic change to the game system. Its not necessarily making new abilities more expensive.
As for roleplaying! Yes, I've played DnD, though not much, I got into other roleplay games though, and eventually ran my own in my own little intellectual property. I haven't roleplayed though in probably 8 years though. Ultimately, while I appreciate pure strategy, in games like chess, go, etc. games like this, where you are creating a civilization, with ideology choices and such, are clearly meant to be played with some "immersion". Which, if the player is successfully immersed, he/she is effectively roleplaying, whether they intended to or not.
Hence why I think it was a poor move to make all ideologies and all perk selections completely inclusive of each other, it breaks the immersion, and if I'm not roleplaying a space emperor... well why not just get rid of the graphics, the images, the cutesy/sassy dialogue, etc.?
Thanks for reading, I know its a long post.