Well that deleted scene had Cap's body frozen in a block of ice, while the movie had him in Skull's ship. I'm glad they cut that part out personally. I mean, leave the suicide in, but take out the Cap easter egg. I do wish they had left some of the more dramatic moments in, like Banner's talk with Doc Samson by the fireplace that was in the first trailer.
I think what happened was Marvel was over-reacting to criticism of Ang's version being too slow and cerebral, so they wanted a tighter script with more action beats and less time for introspection.
At the end of the day, I think both parties are equally to blame for Norton not coming back. Obviously Marvel has more to lose because this isn't just a recast like Rhodey in Iron Man. Norton was meant to be as big a headliner as RDJ.