When ever a product as complicated as a MBP is designed a variety of factors come into play when determining the final design. (materials, components, costs, manufacturing considerations, ergonomics etc.) Decisions often have to be made in favor of one factor at the expense of another. There are, fortunately, ways around the 'problem' you have mentioned and I suspect that the Apple engineers were aware of that when they made their final choices.
I have included some representative examples of the options that are available to surmount this problem.
I am not necessarily endorsing these particular items. Cables should be as short as possible. I use one that is six inches long.
The USB ports are close together because there's very little space in the MBP case design to fit all the ports into. If you look at what's inside the case, you'll see at a glance that the right edge of the case is fully occupied by the optical drive and hard drive; the front edge by the hard drive and the battery, the back edge by the display hinge, cooling vents and airport card (inside the hinge cover), and only the portion of the left edge that isn't occupied by the battery is left over for ports.
There are many USB devices and plugs that are narrow enough to use side by side in the MBP's USB ports. You need to be careful to buy those from now on, not just any USB cable, flash drive, etc.