It is completely impractical to compare this with a space shuttle re-entering. The mass difference alone makes it a completely different problem. Also a space shuttle burns tons and tons of rocket fuel in exchange for altitude and velocity. This requires a lot of energy - energy that when it needs to return to Earth the space shuttle needs to get rid off, it does this by converting it to heat.
For this project, a balloon is being used to provide the lift. This gives it the potential energy of height, but not the velocity needed to retain orbit. Once you take away the lift- you return to Earth. Coupled with the massive weight difference means there is no where near as much energy that must be converted into heat.
A skydiver reaches terminal velocity as a result of their mass and surface area presented to the relative wind. Terminal velocity also depends on air density - altitude and temperature. So a skydiver can go faster by increasing their mass, reducing the cross-sectional area presented to the relative wind or jump from higher altitudes (or on warmer days). In fact even from an altitude of 13,000ft a skydiver will reach terminal velocity after 1000ft and then gradually slow down as the air density increases. Felix will be seeing this on a much grander scale - less air, higher terminal velocity but less friction.
Also the speed of sound is slower at higher altitudes because the air is thinner. Some sources actually credit Joseph Kittinger with breaking the speed of sound at his altitude.
There are various problems that must be solved for this to succeed, but I think its entirely possible and I am looking forward to seeing him pull it off.