The flaw in the Founding titans power.

Its stated multiple times in the show that the Founder has absolute power over all Eldians and titans/titan shifters. And this is technically the case. But the flaw in its power is the fact thats its not precise, it cant just pick a single titan/shifter and un-make it, or remove its titan power, it has to remove ALL titan power. Its why when Eren undid the titan hardening on the walls to begin the rumbling, he had to remove all the titan hardening everywhere. Its why Reiners armor fell off, its why Annie's shell shattered, all at the same time.

Its also possible Eren just didnt have any finesse with the founders power, he technically only had it for a few seconds before he formed his doomsday titan, but he and Zeke were in the paths for years. Before they even went through Grishas memories, Zeke said hed been waiting for Eren to wake up for 4 years. Which means they were in there for years and years, Eren also had enough finesse with the power to completely overrule Zeke, he was able to steal it from Zeke and basically lock him out.

So I dont think its a stretch to say the founder isnt perfect, its got a major flaw in its power. The inaccuracy, it can only majorly change things throughout all the Eldians. I think this is also definitely the reason he didn't change Connies mom back as soon as he gained control of the founder, and the reason he didnt change the members of the military back to human. He couldnt, he cant just pick a certain group of people and change their biology, he has to change every single Eldian, which would also explain why he didnt take away his friends titan power to stop them from stopping him.

Now that last bit was also because he wanted to be stopped, but i think if he couldve he wouldve. He wiped out almost the entire world, he wasn't just too empathetic to kill everyone but his people. He told his friends he wouldnt stop them, because he couldnt. If he were to take away their titan power, he wouldve had to remove titan power from everyone, which would include himself, Zeke, and all his pure titans. (The wall titans aren't the same as colossals, they're just humans that got turned into pure titans, but instead of the regular pure titans, the king at that time used the colossal bodies.) He also couldve killed his friends, but he cared about them too much to just execute them to complete his mission.