My two cents:
I prefer to use flat (or 1" MAX riser) bars for a commute bike; the controls are beneath your hands--
where they should be! Brifters work, bar-end-controls are OK, but these are normally used on drop bars ONLY (I see few--if any--bullhorn/cowhorn bars in use-even by messengers!). By being forced to stay somewhat "heads up" in traffic, especially in urbanized areas (where most bike commuters live and work) could very well be a life saver!! Any lost "efficiency" really makes no real difference for most bike commuters. (It also allows one to wear, in winter, the
much warmer and more potentially protective), full-face helmet!!)

(If you have small hands, like I do, road bike controls, especially the brake levers, can be difficult to reach--no good in an emergency, of which there are plenty!!)
I also give my vote for panniers and/or a rack trunk to carry the load.
Get a
good, rechargable battery head (and tail) light setup if you
ever expect to be riding after dark!!

Any type of pedal is OK most of the year; BMX pin-tread platforms , rattrap, or quill pedals (the latter two fitted with Power Grips or toe clips) in the winter (these, in cold and ice are normally both warmer (no place for the cold to get in at the sole) and safer (you cant "freeze" your shoe into the pedals; I've heard it can happen with clipless pedals). If you wish to use bike shoes, get
touring style bike shoes with a "waffle" type tread, or the similar style walkable shoe used by spin class denziens; you will walk more than you think!!
Second the idea of a yellow/ safety orange/ lime green vest or jacket (or a combo of these!). If you change at work or need an "overpant" (foul weather and/or dusty road use), stick with these, or other, obnoxious colored versions!

Don't give the "motoring primates" (as Chris L would say) any excuse for
NOT seeing you!!
Use any frame type you wish as long as it can accomodate the type and width of tires you want to use, and can handle the stuff you need to carry. Get tires with Kevlar (aramid) flat protection and, if your roads are overloaded with flat producers, thorn-resistant tubes as well, to minimize the need for repairing flats. You want to minimize the chances of having to repair a flat in stormy or cold weather--or in a "sketchy" area of town! Slicks are best in the warmer weather, or if the roads are clear (and the weather forecast doesn't predict winter precip. before you are safely home) in winter;in winter try cyclocross tires (700c wheeled bikes, knobbies (559 MTB wheels or 20" BMX (used on some folding bikes)) or studded tires (700c or 559 (26" MTB)) wheels. BTW, what tires you choose, in winter, depends on the conditions, especially in colder climates; use another bike or extra wheelset(s) in the winter.
Carry a small, compact, tool kit, a spare tube or two in the needed size(s), and a pump or CO2 inflator.
Also cab/bus fare or a cell phone (to call for a ride) if all else fails.
Remember, you ARE A VEHICLE! Follow traffic law--and DRIVE (RIDE) DEFENSIVELY!!