I agree that MIDI is past due for an overhaul, but with most hardware instruments produced in the last 10 years with on-board USB, it renders the MIDI spec as a non-issue. FWIW, think of MIDI as a musical word processor. It basically just records keystrokes. The piano roll, event editor, staff view, they all just display the keystrokes in unique ways, but it's just keystrokes.
Yes, MIDI was just designed to connect an outboard controller to a computer. That is one reason that it needs upgrading. But no, USB connection does not come close to replacing the MIDI spec. USB just carries MIDI data to and from your keyboard in a somewhat less flexible manner. USB through?
If you are editing a MIDI track in Sonar, you are not using the electrical spec at all, but you are using the control spec, as are all of your softsynths. If you are using the piano roll or the event editor, you are using MIDI, not as an interface, but as a programming language, modifying the code in what is unfortunately, not the best imaginable code editor. As someone who has used Cakewalk sequencers for a long time, my biggest complaint is that the midi aspect has not advanced while the audio has been given massive attention.
Still, I can program midi performances that not only I can not perform on a keyboard, but no one could perform, writing code to control instruments that can make sounds of such rapidity and duration that no human being could manage with a metal or wooden instrument, and with the kind of subtlety that is simply not available from a midi controller manned by a performer in real time.
Even if you think of MIDI as a word processor for music, I imagine you are not old enough to remember when a letter had to be typed correctly the first time and could not be duplicated except by interposing a thin sheet of paper impregnated with carbon dust and a binder, to yield at most two or three readable copies. The ability to produce easily editable copy was an enormous advance. The ability to step out of a keyboard performance and move and alter phrases with such flexibility is of inestimable value.