DarkFather said:

Also, the Vader reconstruction scene was inconsistent with the OT in that Vader was shown to have no problem breathing without his mask. In ROTJ we're told he'll die without his mask.

He was leeching from the dark side in order to sustain himself on Mustafar. However, it wasn't a permanent solution. It took immense focus and energy. To have that focus broken for a few minutes is fatal (also explains why Vader was able to survive without his mask intact in TFU after his duel with Galen Marek). That's why the medical chamber wherein the reconstruction took place was pressurized, acting as an "iron lung room" of sorts, just as the meditation chamber we see in ESB was pressurized.

EU excuses. The reality is that ROTS was at odds with the OT here, just as the PT is often at odds with the OT. Lucas should have shown Anakin having trouble breathing on Mustardfart and had the emperor get him a breathing mask there on Mustfart and Vader should have been hooked up to a breathing machine when he was being worked on afterwards. TFU was following ROTS's OT-ignoring precedent.