I've found that I can take over an entire galaxy without ever needing to build or research anything military, Whilst I really like that you can win territory in a non violent way (giving complete domination a more insidious feel) I've noticed that I can bring entire civilizations to their knees and the governments controlling them are fine with it, in fact they're overjoyed and love it. Surely annexing planets would result in some kind of diplomatic wrath? I mean, individuals being influenced are happy about it but wouldn't governments and those loyal to the other race be furious? Your're directly taking from them what amounts to a lot of resources and prestige. Taking enough planets rightly be seen as a threat to their existence and even an act of war.
Some balancing issues I can think of is the removing all diplomatic penalty to close boarders with an early ideology bonus, this seem unreasonably effective. I don't know how the boarder penalty system works but it would make sense if it scales with the number of adjacent tiles, rather than completely negating the diplomatic penalty why not make it reduce the penalty by 80%. So if you've got a massive front of 100 tiles pressing against them they'll be a bit intimidated but still grumpy about ii when it comes to signing treaties.
In the same vein the ideology bonus that makes you immune to influence takeovers is quite overpowered, mainly because in the large maps (like immense) the AI is far far more likely become immune to influence due to the sheer volume of planets (and so free ideology points). Making the bonus increase the time it takes to be converted 5 -6 times longer would seem fairer as it no longer stonewalls a non violent strategy in large games and still gives the encroached planet time to increase its influence with emergency star stations and such.
Also, star-bases in other races territory should be a no no, or at least not too close to their captured stars. I've been building starbases in the center of 3 "neutral" planets orbiting a sun screaming propaganda at them ceaselessly in order to assimilate them, I can't think of a much more aggressive way of non violently taking over short of landing a colony ship on the planet and telling them we're now roommates.
So yeah, I really really like the idea of being a race of apparently friendly people who slowly undermine their allies with aggressive cultural messages, It's fun to watch the influence ripple around a planet imagining my diplomats sweet talking their government by playing space golf, eating those exotic worms I killed a while back and laughing at those poor Terran who got crushed by the Drengin but at the moment it's just too easy.