2) Some mathematicians have identified a probablity problem with evolution. So many things would have to line up so perfectly, that while the world we see around us might possibly arise from non-directed processes, the odds of that happening within justa few billions years seem remote. A good way to discuss probablity and mathematical analysis in science with students.
3) DNA has been considered to carry a lot of "junk". But some scientists now think it's not junk at all. How much do we know about DNA? We develop theories based on things we do not fully understand -- these are necessary hypotheses, but let's make sure students understand the difference between a hypothesis created from partial information and a proof based on repetition in a lab.
4) The Cambrian Explosion is a unique event. 530 million years ago most major groups of animals suddenly appeared. Why? Does evolution help us understand this event? Such an event has not occurred since (at least on that scale). Why not? Does evolution help us understand why not? What are the limits to evolutionary thinking?
Please note: My four points above are not my attempt to "prove" that evolution is "false". I merely wish to point out that there are interesting areas that can be explored and that students can gain a better understanding of how to "do" science, and what it's limitations may be, if they explore controversies within a given scientific theory.