After much reflection, I've drawn up my personal list.
Above average films - strengths:
1. TUC - characterization/plot (c/p)
2. TWOK - c/p
3. TMP - starship porn/music/science!
4. TSFS - c/p
5. TVH - c/p
6. First Contact - c/p
Below average films - weaknesses:
7. TFF - bad fx/science/humor but major bonus pts for soundtrack & "pain" scene
8. Generations - plot/Kirk's death
9. Insurrection - plot
10. Star Trek (2009) - bad science/Vulcan destruction/Kirk's leapfrog promotion
11. Nemesis - characterization/plot
12. STID - characterization/plot/bad science/Khan?!?
Honorable Mention (not ranked):
Note: I am not a JJ hater, it just so happens that I find massive flaws in his films as well as the TNG films with the exception of First Contact. I truly hope he can turn the page with next film and produce something more original, thought-provoking, and entertaining.