I just read it in one sitting this entire morning. 
 I think it really helps to have read the short story before, so I knew the plot and everything and could follow Charlie's progress more closely. Lots of other areas were explored too like his relationship with Alice Kinnian, moral dilemmas, etc. 
 I think after I've thought about it for a bit, I'm going back to it soon and read through it more slowly. 
 Lots of things for me to think about: the quest for intelligence, how it affects other aspects of his love - love, friendship, connecting to other people, etc, of Charlie's emotional growth/journey, the idea of two persons? existing within one body, appearance/fear of being judged by others - as seen in Rose as well as all those scientists like Prof Nemur - which is linked to arrogance/risk-taking and not judging others without understanding their situation, and so on. Other more minor stuff: what really is IQ, the Gimmy moral dilemma, etc. 
 Go read it. (And the short story too!)