For handling the characters, my vote is split between Nimoy and Frakes. Both men knew the characters better than any outsiders and both men gave the cast bits of business which didn't make them look like idiots. Frakes has the edge in directing action, his work in FC and INS is excellent.
My issue is that at around Trek 4, the directors simply HAD to come up with the story as well. This led to Trek 5 and I wondered why Paramount, which "had" to give Shatner his shot at directing, let him originate the story. Nimoy had better instincts as to what made a Trek story, but it just seemed weird that this "director as story guy" bit was suddenly assumed. As such, the quality of the films dropped and everyone got all jokey.
What amuses me about this thread is the argument over which Trek film is more "deep and mature." For all of the chest beating over the "exploration of God" in TMP, it was really only mentioned in a few lines of dialog - some of that was only in the TV / Extended Edition. The film was primarily a reunion, V'Ger travelogue. You can blame Wise if you wish for trying to make Trek into 2001, but he didn't write it. The film started shooting before the ending was written, and the script was pretty thin, character-wise. So what choice did he have but to give it a sense of wonder? Years of re-viewing and reflection have made some fans see a higher purpose, but it's really not anything more than warmed over SF; a rewrite of an old "Genesis II" script. I love the film, as much as it might seem otherwise, but I am well aware of its limitations (as well as its strengths).
TWOK is Moby Dick mixed with Kirk's mid-life crisis. It's got action and good performances, but it's not any more or less profound than TMP. It gives some meat to a couple of the characters, but aside from Kirk and (thanks to the DE) Scotty, nobody else really benefits from it. However, it's got the fell of a John Meredyth Lucas production (which isn't bad at all).
Both films have heavy influences from past and superior films and books. TMP shoots for art and TWOK is space opera. Neither one qualifies as a cinema classic or has uber intelligent scripting. Both say what they have to say and are equally deep/shallow. They just say it differently.
And let's not rewrite history: the general consensus among critics, fans and those who worked on TMP was that it was boring. No matter what high minded subtext you want to find in there, the presentation was slow, ponderous and self important. It was not seen as "good" and was the poster child for how NOT to make a Star Trek film. It finished Roddenberry in Hollywood until TNG (not that he was a major force there to begin with), tarnished Robert Wise's resume and gave us the phrase "10 years for this?" It only made money because fans were desperate for any kind of new Star Trek. This was a one-time thing, as later box office disappointments have proven.
TWOK, for all of its action and pathos, was the response the studio had to the backlash. It was a 180 degree turn and the overwelming reaction by the same people as before was super positive. And then we had the phrase "now THAT's more like it!"
Both films are enjoyable and both have amazingly glaring flaws. They are equally good in different ways. But if you want deep Sci-Fi, Trek movies ain't the place to look.