The objective is to get from point A to point B every day, minimizing some combination of time, effort and cost. The objective is not to get exercise (in that case, take a longer route, make the bike heavier) or to win a sprint. If cost is not a concern, then of course get the best bike money can buy. It is still not obvious this should be the fastest road bike.
The total time spent on bike commuting includes maintenance, locking and unlocking the bike and any other unavoidable tasks. A high-end road bike with thin tires may save some time every day, but gets flat tires more frequently than a thick-tired mountain bike. Each occasion of a flat tire costs significant time, plus some money. The time cost occurs randomly, which for most people is worse than if it were predictable and could be scheduled.
Thin wheels get bent more easily than thick ones, again requiring maintenance. Thus the fastest commute is not achieved by the lightest, thinnest bike. Reliability is what influences both time and cost the most.
Wheel and tire width affects weight, aerodynamic resistance, rolling resistance, flat tire and wheel bend frequency and ride comfort. The lowest rolling resistance occurs when the tire pressure is such that vertical tire thickness drops 15% under load (F. Berto, Bicycle Quarterly Vol 5 No 1). Tire tread pattern has such a small effect on rolling resistance that it can be ignored for commuters. The tire thickness that minimizes rolling resistance is 22-23 mm (wheelenergy.com). The thinner the wheel and tire, the lower the aerodynamic resistance, but this effect is under 1% of effort, small enough to ignore for commuters (http://www.biketechreview.com/index.php/reviews/wheels/63-wheel-performance). Wheel weight and inertia have an even smaller effect.
The thicker the wheel, the less chance of it bending (other things equal – wheels of weak material or poor construction bend no matter what). More expensive wheels are on average stronger and lighter. The thicker the tire, the lower the probability of punctures and pinch flats. For a commuter, it is optimal to choose wheels and tires heavy and thick enough to never bend or get flats on normal roads (having some potholes, broken glass etc). In my experience, this means thicker than 25 mm road tires and thinner than 50 mm mountain bike tires.
Punctures are less likely than pinch flats even with 25 mm tires. Puncture probability can be further reduced with e.g. Kevlar-lined tires, which add less than 40 dollars to cost.
It sounds like I am advocating a hybrid bike – these have intermediate thickness wheels and tires and are supposedly designed for commuting. My experience with the one hybrid I tried (Apollo Trace 10) was very bad. Both wheels bent enough to hit the brakes in less than a month of half an hour per day riding and two spokes broke on the rear wheel. Looking closely at the wheel, the substandard manufacturing was obvious. My speculation is that hybrids may be low quality because they are marketed to people who on average are not bike fans, ride little and in flat road conditions. They thus cannot distinguish quality levels and may buy a bike mainly based on its flashy paint. Road and mountain bikes, on the other hand, may be bought by more knowledgeable customers. For these to sell, they may need some minimum reliability.
It would be good to have bicycle reliability statistics like there exist for cars. Then this would be the best source to base bike choice on, not recommendations from friends, forums or bike shops.
What matters for speed and ease of riding is first the fit of the bike to the rider and second the maintenance of the wheels and drive train. The weight and general flashiness of the bike are far less important.
I think that the best used bike for a given price is better than the best new for that price, because clueless customers go for new, and some people want to demonstrate their wealth by replacing their high quality used bike with new at short intervals. They sell a high quality used bike for cheap to make room in the garage. I got a great on a used bike: a like-new 2008 Giant OCR 1 for 350 AUD. But this is just one data point.