Well, I mean.. you saw Vader's skeleton outlined by the lightening. It may have been 'unfocused' but it was clearly causing serious problems since we could see his freaking skull.. not to mention just a split second of uncontrolled electrical surge is enough to fry my computer, I'm not really shocked that 4 seconds of sustained, unregulated, high voltage would screw his portable life support system.
<edit> also, the Emperor wasn't directly trying to kill Luke, he was toying with him, torturing him. I always assumed (admittedly with no evidence) that when Vader picked him up, Palpatine dialed the juice up to 11. /edit.
But that's just me.
for me, the thing that is good about the PT is that despite it's many, many flaws, it still provides context for the characters, their arcs, and history, and at least for me, made Jedi a better movie (no, not because the PT sucked) because it made the emotional climaxes more fulfilling..