The single most dramatic improvement will be the lighter wheels and tires as others have said. Plus you can always transfer these to another bike.

But for commuting I disagree with the clipless pedals and shoes idea because a lot of commuters work in their shoes they rode in on, and clipless shoes will be very uncomfortable to walk around in all day-or you have to carry your work shoes with you in a backpack or pannier. Thus with regular pedals you can wear any shoe you want. You can get adjustable straps to help keep your feet on the pedals for better power transfer, with those any shoe will work.

Anything else you want to replace is up to you. Your suspension seat post you may like because it dampens pot holes etc. Seats and handlebars? If you like those already why replace it?

You mentioned the derailleurs, are they working fine? If not maybe they just need to be adjusted properly, but if their old and tired and all the adjustments in the world aren't helping then replace them; but derailleurs will not improve your ride noticeably.

Of course a newer better bike is nice to have, but you mentioned you commute to a high crime area, so why buy a better bike to commute on? Just replacing the wheels won't make the bike stand out because if your commuting then in a few days water and dirt will be on the wheels and no one will know their new!

I knew a guy that took a bike he had and beat it with a chain to make it look unappealing to thieves; it must of worked because his bike never got stolen. If theft is a problem make sure your using two different kinds of locks on your bike.