I stumbled upon that Chud article earlier -- it's a terribly written, juvenile mess that seems to think the story originally presented was good. It wasn't.
Frankly, the film should have been about Connor right from the get-go, instead of Marcus. Who the hell cares about Marcus? Audiences know nothing about him. But they do know Connor and Reese. Explore that dynamic instead.
I don't think it's really Bale's fault this film got tampered with. It was a bad script right off that just got more and more muddled and messed up as other writers took shots at it. That's a producers fault, not a star -- even if said star wants rewrites.
I think you had the right idea with your last blog -- this film was ruined because Warner got gun shy about an R-rated summer vehicle following the dismal performance of Watchmen (which shouldn't have been a shock to them), so they sliced and diced the heart and emotion out of the picture and gave fans a stripped-down PG-13 action picture. If times weren't as tough right now, Warner probably wouldn't have made that call.
I really hope we see a Director's Cut in the future.