I'm not qualified to tackle your list, but I would like to know what is wrong with the methodology of sciemce as currently practiced.
I would like to know what ongoing research should be cancelled, and by what replaced.
Your posts strongly suggest that something is wrong with the practice of science.
2. Scientists are forced into a gauntlet of peer review to publish. Einstein and Darwin neither were required to do this and several Nobel prize winners were originally rejected. (Refereed Journals: Do They Insure Quality or Enforce Orthodoxy?) IMHO, the publications which are rejected for content need an outlet to encourage the innovative thinkers.
3. Scientists who promote their own political, social or ideological agenda should be labeled accordingly (a disclaimer) so that consumers, grant makers, alumni, etc. will know the difference. This is generally done for all scientists in the Intelligent Design and YEC ranks - but Pinker, Lewontin and Singer also come to mind.
4. There needs to be more generalists in science. Everything has become so specialized that the bark on the trees are screaming to us and yet nobody seems to be able to capture the entire forest since the early 1900s the Godels, Einsteins, Heisenbergs, etc.
5. Science either needs to quit making theological pronouncements altogether or step into it with both feet, giving equal consideration to both the atheist view and the intelligent design view.