"I originally wanted an ending that would leave shadows in the readers’ psychological views. For example, in the movie The Mist, there is a scene where they killed off everyone that was seen without any differentiation (i.e. people were killed regardless of what role/morals they had); at the time, I wanted an ending similar to that. But now, since there’s been a lot of support since the anime, I feel as if I can’t draw such criminal-minded, malicious material, and I’m beginning to doubt if I want an ending like this as well.”
And putting aside my general sentimentality and passionate attachment to a number of characters in this series, I think this is fantastic. Because stories evolve as writers write them, and I get the feeling that seeing his characters through the eyes of others when AoT became an anime might have increased Isayama's own ideas of and affection/mercy for his own characters. For example, take that cover of Bessatsu Shonen Magazine that shows Eren in both manga style and anime style. Just the difference in expressions between the two Erens shows such a vastly different view of the character, though both are true faces of Eren Jaeger. It's just interesting which one Isayama chose to show and which one the anime artist chose to show.
Based on that and my own general impressions, I think manga!Eren was Isayama's "id"--an almost allegorical representation of humanity's lot and a vent for him/people to rage against how puny, fragile and futile we ultimately are in the grand scheme of things. But then, through the anime, Isayama finally got to see Eren from an external view, as his own person. I think seeing how other people respected and cared for Eren and the other AoT charas might have helped Isayama see the beauty of his own characters more (and perhaps, feel the tragedy of the horrible deaths he'd planned for them more). So I think it's very possible that his changing of the ending is a natural evolution of the story as his ideas/understanding of his own characters grew, and might actually be the "truer" ending now, based on the story as it has been written to this point.
Personally, I'd love it if he pleasantly surprised us by giving some of the characters a happy ending. After the long, long "night" of the titans' reign of terror, it'd be nice to see our heroes have some happiness.