A couple of the most obvious things:
We must teach critical thinking to all students. I've been in (and taught) too many introductory courses where the class is an exercise in rote learning, rather than thinking. I think it's more important for beginning biologists to master the art of comprehending what they are doing, rather than being able to rattle off lists.
Students' writing and communication skills must be improved. OK, this one makes me feel guilty. The one thing I had to cut from my new course was writing: I've got over 80 students, I'm writing all new lectures, and I have no TA help (not that you'd want to use TAs for grading writing), and I couldn't possibly handle student essay writing on top of it all. I console myself with the fact that our curriculum does have a strong writing component in subsequent courses.
Read the comments as some of the readers make further suggesions.
How to Teach Science offers up suggestions and plans along the same line and I'd highly reccomend it to anyone trying to navigate science without a curriculum (as so many secular homeschoolers have to do).
Another note, the post links to an excellent issue of the McGill Journal of Education which tackles the subject of teaching evolution. It really is an excellent read.