I definitely feel that there are some intricacies to influence flipping that are greatly improved with some of the new features (free trade. more treaty options, etc) making going to war over a flip a more difficult decision . I don't see a point in discussing the admitted basic beta AI though & will go into other stuff. One place simple deciding to secede from its union/monarchy/etc to join another is rarely a simple matter... Russia, Turkey, England & the island nation of Cyprus are very twisted about & complicated even just looking at the time period from ww1/2 on to today.
Rather than just getting a message where planet xyz has joined/left after you click end turn, I'd like to see a bit more control & potential negotiation over it
You have to be able to look at the planet wanting to join/leave to see what's built there prior to starting the negotiation. I'd like to see the planet(s) first negotiate with the faction they are leaving (if they are happy) or the one joining (if unhappy) to help determine their feelings towards each major race before splitting them into a minor race. Start with alliances & allow that alliance to degrade/absorb the minor race. If multiple planets are expecting to & later wanting to flip in a short period of time, have them secede as a group to a single minor race. If the major race is later wiped out, maybe give their UP seat to the surviving minor race.
Maybe those initial negotiations involving the minor race still remaining under the parent race but doing things to prep for standing alone (rearranging colonies/building shipyards/etc) and industrial/military point trade. Freeze the minor race for a number of turns & if they want to flip again later, allow them to.
A lot of this is way more than a minor suggestion & more of a gcIV type possibility, but having them fork into a minor race locked that way for X turns that get reset/extended each time a new planet/starbase if influenced into being dumped on the minor race could add some depth to the process of influence flipping since even in galciv2 it was possible to build up influence in a way that just grew at an unstoppable rate resulting in "yea I don't see any reason to bother with the cleanup here>new game". Having them fork into a unified minor race might not be so significant a change