Personally I think the Pragmatic tree is too strong with its diplomacy tree down the bottom, I would suggest changing the "100 turns of peace" to maybe giving you access to a special one time only power that will end all wars you are currently in and prevent them from restarting for maybe 20 turns? It would have similar utility but it wouldn't be as strong, especially not for an ability which is tier 1.
Culture is far too easy to develop and expand, especially with the factions that have influence bonuses as race bonuses. I would suggest adding a modifier to your influence, if your empire has x influence it requires more influence to expand then it did during its last expansion. The modifier gets harsher the bigger you are, which will prevent rapid expansions from chain planet revolts. I won a game without a single war or ship blowing up just by using mass temples and culture starbases. Its just far too easy.
Add a building to the influence tech tree which will increase the time it takes for the planet to revolt
For each planet your opponents lose to your oppressive culture they will become more aggressive, when I played it the Dregin and Yor just sat back and just happily waited for my culture to consume the galaxy even though if they had teamed up they would have pulped my empire.
Add culture technology that increases resistance to enemy culture making it harder for them to push you
Add culture technology that will decrease the expansion penalty on cultural boundaries.
Decrease effectiveness of cultural upgrades on starbases until either a bolster technology is researched or obtains a x quantity of resources.