Could have sworn I saw someone else add a few on. But I would add 8. The dark and adult feeling to the film. I did not come out of the theater feeling like I just saw something catered to family friendly audiences, which I appreciated. 9. Picard admitting that he was tempted to take Shinzon at his word but acknowledging that he could not allow his personal feelings to sway his judgement. 10. Finally... a REAL cloaking device which couldn't actually be seen as a distortion, disabled by a technobabble energgy pulse, or tracked by the ships impulse gas.
Totally agree, TVH, whilst successful and entertaining also marked the point where we began to laugh at the characters rather than with them from time to time. TSFS had it's moments of humour too, but nearly all of them were well judged and were integral to the plot, like you say, the JJ movies have a similar balance to them also.