3 is better than many give it credit for (I'd give it an 8.5), but it wasn't as well composed as 2 was. The writing and development time were its primary sources of weakness imo. The villains were underdeveloped, game handling had issues, Hennig herself stated that they wrote the story after the setpieces rather than the other way around (leading to stuff like the massive red herring of the ship section, however impressive technically), Nate and Elena's relationship development was paper thin, and the third act was very rushed and underwhelming. Never played the MP but from what I'm told it was also inferior. 2 was just far better paced and put together. It and the original had deliberately hamfisted narratives that were executed well around tighter, leaner, more cohesive campaigns.
4>2>3>1