That was due to the architecture of the Mac-- using toolbox calls and not accessing hardware directly. They couldn't even change anything in the Apple II without everyone's programs breaking, hence why there were never faster processor speeds, new CPUs, enhanced gfx modes, etc. The IIgs, of course, did bring in speed, new cpu, and gfx, but Apple engineers had to spend a lot of time making it compatible with the //e. Not a lot of programs were made to work just on the IIgs. Why bother, said developers, when it already runs the existing II software, and it that software is compatible with all the rest of the II family. Therefore, the innovation which could have happened on the IIGS with its enhanced graphics, sound and CPU, for the most part, did not happen.
Disaclaimer: the above paragraph is a summary of what I've read in various Usenet posts, and is not something I've come up with on my own, though I do agree with it.