I definitely understand why people don't like the story changes, but I don't seem to mind too much. Maybe I'm just letting the Evangelion reference blind me (something something I clapped when I saw it) but this change doesn't seem to far out of left field for what ONE is going for with this so far.
I do prefer the original webcomic by a large magnitude, but honestly they're so different it's hard to consider them the same product. There are a lot of adaptations I consider straight downgrades/upgrades, but this isn't one. I'll look at it the same way I look at say, the FFVII remake.