While rewatching Madagascar I noticed something
The lemur kingdom is completely fucking screwed by the end of the trilogy.
First of all, the second film starts with Julien putting a gecko called Stevie in charge of the kingdom so he can leave with Alex and friends. And the third film makes it very clear that Julien is not temporarily leaving, but instead has absolutely no plan to return. It's very unlikely Stevie is even able to communicate with the lemurs. But even if he is, he has no knowledge of leadership or how to protect a kingdom and will likely just end up running the kingdom into the ground. Especially since the two lemurs who were the ones holding back Julien in the show "All Hail King Julien", Clover and Maurice, either left with Julien (Maurice) or have retired (Clover). And this is assuming Stevie is even able to keep his thrown. There's a number of Julien's family members, leaders of other kingdoms or even just random lemurs in Julien's kingdom that would love for an opportunity to takeover the thrown. Given how we're been repeatedly shown just how easily the lemurs in Julien's kingdom are able to be swayed by someone who's just good at talking (they voted for someone literally called King Julien THE TERRIBLE who ATE BABIES), it's very likely someone will try to overthrow Stevie and will probably succeed. And given how almost everyone in Madagascar is shown to either be just as, if not more incompetent than Julien, or outright evil. It's likely whoever overthrows Stevie will be bad news.
Then there's the fact there's no one around to protect the lemurs anymore. It's made clear in "All Hail King Julien" the two main reasons the fossa weren't attacking the lemurs was because Mary-Ann had a position in the tribe, and because Clover was protecting the kingdom. By the end of the series, Clover is retiring and Mary-Ann has lost her position. Then it's made clear in the movie the fossa are avoiding the lemur kingdom due to Alex. Now I ask, how long until they realise Alex has left along with Julien, Maurice and Mort? And how long until they decide this is the perfect opportunity for an all out attack? Granted, in the second episode of the series they show they're able to protect themselves without Clover. But how well will they be able to protect themselves without a leader that can motivate them around it? Even if Stevie can talk he's certainly not the ultra charismatic King Julien and would likely do a very poor job organising the kingdom to defend against the fossa, leading to many casualties.
And now for the final and arguably the biggest reason the kingdom is screwed is due to the ending to the third film. See, this film introduces Chantel Dubois, a French animal control officer and the one thing this film wants to get across is that she's ULRA competent. Before the events of the film, she's been hunting animals since she was 7, she has a perfect case record, has an extremely heighten sense of smell, was able to jump between buildings, do a matrix style dodge to avoid bananas and effortlessly ran through several fucking walls. She also has a team of four people working for her, and when they get injured, she fucking SANG to heal them. Granted the heroes do still beat them in the end, but only with much effort. Plus they have the penguins on their side, who might be the only beings in this universe more powerful than Dubois (probably Mort as well but his eldritch abomination powers weren't revealed yet). But once they finally defeat Dubois what do they do with her? Do they arrest her? Do they kill her and her men for their crimes against animal kind? Nah, they send her to Madagascar. Reminder, Madagascar is full of small animals that are NOTHING compared to a HUNTER whose office wall is covered in severed animal heads that was able to kill a snake when she was SEVEN. Now, I have seen it mentioned before she could've been arrested by Madagascar authorities after arriving. But we saw how well arresting her worked in the third film, let's just say, it didn't work at all. If she is arrested, she'll easily breakout and then be on an island covered with animals for her to hunt. Including the lemurs who will be the easiest target since they have no leader and will absolutely struggle to defend themselves as a result.
TLDR: if you're the leader of a kingdom and want to runaway with a lion and his friends, don't make a gecko the ruler in your place.