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.
You're in for a long road if you think scifi movies have to have a lot of accurate science in them and use that to rate quality in a movie. It's not as important in entertainment to be accurate, as Star Trek is often not, but what is more important is that some of the better movies use what we might call the standard "scientific method"(in the case of STTMP--which you label as scientific--it has precious little science in it, but it does have a police procedural feel, and it's speculations seem plausibly scientific even if they are not). If they are innacurate but seem internally consistent with their speculations I can suspend disbelief. By this gauge, the distance between STID and STTMP is really not that wide, and STID does far less of what many people thought Star Trek was doing too much of...technobabble! It is enough that they discuss something without explaining it in detail. The technobabble was taking casual fans out of the equation.
Frankly STID's stance on drones is far more thought provoking than just about any theme tackled in the previous ST movies, far more so than the after-the-fact and obvious fall of communism plot in STVI for example.