Even now, I'm still feeling bad for Maruki because dude just wanted to help people. And in a way, he's just like the Phantom Thieves, but the core difference is that the PT don't rob people of their future. Freedom means being able to fly or fail on your own merits, and even though he gave them the perfect ending, it also means that he took away everything that made the Phantom Thieves who they are. It's not necessarily a "wrong" choice, but people have to ultimately come to terms with their own pain and struggles in order to grow stronger. The PT gained the power of using their Persona because of their spirit of rebellion and accepting the power within themselves. All Maruki wanted to do, in the grand scheme of things, was run away because of how painful his life was. And while it's super real and understandable (I'd wager most human beings do this), making everyone "happy" via his methods doesn't truly answer everything in the long run.
It's like asking, would you rather a lighter load or stronger shoulders? I don't think either answer is wrong, because everyone's different. But to take away the fundamental part of what life is all about... It's not the answer. A world where everyone is happy is a wonderful thing to aspire to, but views clash all the time. What would Maruki's answer to stuff like that? Even in his Palace with the psychological evaluation, it's all about what HIS stance would be on certain matters, not taking into account that not everyone has the same view (even if they still may be in overall agreement). That's why Akechi of all people rejected it, because if you're forcing people to have the same viewpoint as you and just be "happy" without their willpower or efforts being considered... That's brainwashing. None of it is "truly" real. But then again, in a series with different worlds regarding shadows and mystical powers involving the inner strength of oneself... What really IS reality, anyway?