The fact that Khan and Kirk don't meet in person is what ELEVATES ST II. The movie is about more than two old men (or women) fighting on scaffolding, a device used in every TNG movie. I will not even dignify the idea of Nemesis having the 'best villian' far from it.
I would say Khan and the Whale Probe win, trek fans love Khan, the casual fan knows him (KHHHHHAAAAAANNNNNNN!), and they also loved and remember 'The One With The Whales'. Those clearly caught the zeitgeist and win in my book.
I don't think your argument for the what probe works because I don't think the non-fans who saw the movie even registered the thing--most of the movie (and all of the "funny" stuff) take place in 1986 with the probe nothing more than a vague threat. People didn't like Trek IV becasue it had a good villain (full disclosure: I despise TVH) but because it was a light and breezy romp.
You're right about Trek II, though--far better w/o a contrived face-to-face.