OK, the Space shuttle tank has a big LO2 feedline running down the length of it to carry the oxidizer to the engines. It is much more complex to put this through the interior of the tank, and a huge safety risk. If either leaks, LH2 and LO2 will react to form water, but extremely vigorously
So in this case, the inefficiencies are made up for in ease of build and safety.
Also, it only takes a couple/few minutes for a rocket to get high enough that aero loading isn't an issue.
As far as the liftoff-from-altitude idea, basjoos is correct about the fuel weight issue. Plus, there's there's nothing to push off from, so it's harder to get started, there's no vertical momentum. You could do it but you'd probably have to burn your engines for just as long if not longer just to get started, so there's no benefit.