I don't think I've thought really hard about questions in more than two subfields of botany. There are hard questions which seem to just snowball since Darwin's times, but from what I can tell, there's a major line of research (comparing various groups of plants using progressively complex machinery), from which theories branch off without much re-weighing after initial rejection.
If it's worth saying, but not worth its own post, then it goes here.
Notes for future OT posters:
1. Please add the 'open_thread' tag.
2. Check if there is an active Open Thread before posting a new one. (Immediately before; refresh the list-of-threads page before posting.)
3. Open Threads should start on Monday, and end on Sunday.
4. Unflag the two options "Notify me of new top level comments on this article" and "