The things they took from TWOK for Into Darkness did pull me out of the film and came off as less honoring the other film than another attempt to bask in its glow, which is something also arguably done with Star Trek 2009.
I can understand your desire to see Shatner and Montalban interact and I wouldn't have minded seeing that myself, though I think the movie works the way it was constructed. And I don't think there could've been an interaction between the two without an altercation. I don't see how the story could be played any differently since Khan was so far gone.
TWOK Khan wanted to hurt Kirk. And being smart enough to not fall for Kirk's challenge to beam down to the Genesis station, Khan decided the best way was to strike at Kirk's friends and ship while he was helpless to do anything about it. I thought Shatner captured the rage of his impotence pretty well, even if his shout was ripe for parody. It was a very powerful moment back then even if it made me chuckle. As for Quinto my eyes just rolled at his homage.