You do realize that in a very short time that newer computers will have no 2D engine at all for acceleration?
Whether anybody likes it or not even your 2D APIs will need to be rendered using a 3D engine for any sort of good performance. So I don't see a problem with taking advantage of it to improve usability.
The R200 ATI graphics engine was released in 2001. The early GMA chips for Intel stuff was released in 2004 or so...
So most average computers sold in the past 7-8 years can support good-enough 3D graphics to support a composited desktop. Even low-end machines made in the past 3-5 years or so can support composited desktops just fine.
Hell back when OS X was first released it had a composited desktop and it had no acceleration at all and it was fine to use.