I don't think Nimoy refused GEN because it was too much trouble to appear on set every day.
He refused because the part he was offered to play wasn't substantial or meaningful enough to be worth the effort. So the question is why his insubstantial and somewhat gratuitous cameo in STID was worth the effort, and maybe part of the answer (though certainly not the whole answer, of course) is that it didn't take much effort. He could've gotten it over and done in a single day.
Besides, at the time of GEN, he was only 63 years old and in reasonably good health. Now he's past 80 and much more frail. He's nominally retired, and thus one has to consider what it would take to get him to make the effort to play a role. His cameo in Into Darkness
reminds me of William Hartnell's appearance in "The Three Doctors" on Doctor Who
-- he was ill at the time and thus only appeared on viewscreens in pre-recorded material that he performed by reading cue cards.