First, let me say that I don't know how the diplomatic effects are calculated and how that translates into diplomacy. At present, all I see are (1) nothing, (2) your ideology is different, or (3) your ideology is the same.
That being said, I would suggest that the diplomatic effects be tailored to a scale of differences. One simple example. I have 5 benevolent traits and 4 pragmatic traits. My neighbor has 4 benevolent traits and 5 pragmatic traits. Sounds like I am benevolent and he is pragmatic, so we have a diplomatic issue. Isn't this quite distinct from, say, I have 7 benevolent traits (less because cost is higher) and he has 7 pragmatic traits? And isn't this quite different from having another neighbor who has 7 malevolent traits? (Actually, maybe not; see below).
I suggest a wheel not unlike the econ/manf/res wheel.
The three traits are at each corner. We start at the center of the triangle and move in the direction of the appropriate corner when we select each trait, according to how many points we spend. Then calculate the difference between us and them as the distance between us on the "ideology" layout. And then our diplomatic relations are appropriate to how big those differences are. Notice that as the game goes along the differences can get much larger; at the start they will be small (zero at turn 1). Sounds good to me. And the amount of specialization required to get the traits toward the end of a line will necessarily create more diplomatic friction....a nice trade off.
One problem with this is that, for example, two factions both being pragmatic might be quite different because one has more traits earned. But perhaps that isn't such a bad idea. One is more "extreme" than the other --- as below, so long as we do not equate pragmatic with neutral.
This doesn't account for the larger difference between the extreme ideologies and the "neutral" ideology. But as I suggested, perhaps that is just my mindset being wrong. Pragmatic does not necessarily mean neutral. If we just accept all the ideologies as equally antithetical to each other, then no problem. And perhaps that is best, and makes for the most interesting interaction.
I am sure others can find better ideas/have more info on what is actually happening.