I dont see why most people despise this ending just because Aion shows up at the end rendering all the effort shown in the series useless. It perfectly pictures how humanity as a whole is plain stupid and keeps making the same mistakes again, and again, and again, almost following the pattern shown in Hegel's works (aka social determinism or historical cycles)
All in all I think the originality of the ending (for once we can see how evil wins as it usually happens in the real world) partially saves up a mediocre adapatation of the manga... well that's just me
