Definitely Into Darkness. Although I enjoy Wrath of Khan and think it's a good movie, I think it's overrated. I always preferred the fun and adventure of III - that fun and adventure which ID has LOTS of.
Into Darkness was fun but I think Wrath of Khan was better. The series history gave it more substance.
After watching TWOK until my tapes wore out, I had left the movie behind for about a decade. My memories were that it was a bit cheesy, but fun. After STID, I rewatched TWOK with new eyes and it was phenomenal. Every beat was great, the pacing was great, the characters were focused and the story was well built. It really emphasized what a mess STID was. Watch both in a setting and I can't believe anyone would choose the STID over TWOK.
TWOK of course. Better plot, better Enterprise, better guest characters (can't beat the real Khan and Kirstie Alley's Saavik), better all round feel.
I like them both. It's really tough to compare two movies made thirty years apart against each other. The differences in technology, society and audience expectations are astounding.
Wrath of Khan. While on the surface it was a simple enough movie on the surface, it was subtly deep on a lot of levels with the themes of getting old, rebirth, revenge impossible odds and death. Heck, Khan's own bookshelf on the Botany Bay foreshadowed this nicely. The action sequences in ID were no doubt better, but 30 years later that's a given. The difference between the two movies is TWOK used the action sequences to enhance the movie, while ID used them pretty much to carry it.
Has to be TWOK, it was a better story. The story included the "re-birth" of the aging Kirk, and his introduction to his adult child (we knew he had to of had some). The death of a major character that wasn't fixed suddenly by the end of the movie, you had to watch the sequel to see that. STiD had better SFX, but to it's detriment it had too many action sequences. Don't get me wrong, I like to see some, but they should not get in the way of the story telling. The first couple of time Star Trek trotted out "the evil admiral" it was good story telling, by the time of STiD it was cliché and tired. .
Not at all, I thought the death of Pike (even though we seen lot's of deaths before) was depicted quite well. The scene with Scotty in the club bitching with his friend, receiving a call on his "cellphone" was funny and interesting. Scotty (again) stating that he had to sign off on everything that was brought aboard to ensure it did interact with the M/AM reactor made a lot of sense. Really too bad these were such isolated good moments.
TWOK, for all the above, and specifically the Ceti eels brought an eerie, creepy factor that STID lacks.
I do like them both pretty equally. I give the slight edge to StiD which has much more action and adventure than TWOK.
I suppose that TWOK was my favorite of the two though l enjoyed ID a lot. I just felt like Khan didn't play much of a pivotal role in ID as he maybe should have. In TWOK there was also a personal history between Kirk and Khan (though I hadn't seen Space Seed at the time I first saw TWOK) that didn't exist in ID- for obvious reasons (i.e. it wasn't Kirk who initially encountered Khan as in the Prime universe). ID's take on Khan actually- for a short while- made him somewhat sympathetic- being upset (and who wouldn't be?) that Marcus had killed his "family" and I kind of liked Kirk and Khan teaming up with each other (briefly) to go after Marcus. That was a neat twist that I hadn't seen coming- but then as soon as they got the drop on Marcus, Khan went back to being "pure evil" (Kirk was smart enough to realize that he would turn on them but misjudged his ability to keep him down with a phaser stun). I'm somewhat glad that they didn't kill Khan at the end and left open the *possibility* that he may return in a future movie (though hopefully not the next one) as I feel like we got as much of him as we deserved to get. BD did a great job with the role IMHO.
STID. But that's mainly because I utterly detest Montalban's Khan. He's so slimy and sleazy and disgusting, the kind of guy I'd rather throw out the nearest airlock. I much, much, much prefer the ice cold Harrison. That said, I think the movie wouldn't have suffered at all if Harrison had been Harrison, simply another augment gone awry, rather than the remake of a legend. I admit Khan is a legend, even if he profoundly disgusts me.
WoK has more substance to it, with the subplot of Kirk dealing with his aging. And the battle in the mutara nebula still stands up after 30 years. The pacing actually isn't great, it gets off to a really slow start. But it remains a more important film than STID (which was still a lot of fun).