I'm kind of surprised by the choice of the SGX543XT as well. It admittedly hasn't reached market in devices yet, but no longer has the limelight against the SGX544XT and SGX545. The SGX554XT has also been announced and of course the 6 series which is still further out.
Given Apple's previous choice of the SGX535, I too thought that the SGX545 is the next logical choice. These were both designed to fully target desktop graphics standards compared to their cohorts, DX9.0c and OpenGL 2.x in the case of the SGX535 and DX10.1 and OpenGL 3.x in the case of the SGX545 while the PowerVR SGX520, SGX530, SGX540, and SGX543XT were focused on OpenGL ES 2.0 which is a subset of OpenGL. Going with the SGX545 would have allowed Apple more flexibility in functionality since the additional desktop capabilities can be exposed through extensions in OpenGL ES. The SGX545 also supports the full desktop OpenCL profile whereas the SGX54XT3 only supports the embedded profile, which is again a subset of the desktop spec.
At the very least I thought Apple would use the SGX544XT, which adds DX9.0 Level 3 and OpenGL 2.1 support to the SGX543XT. It was also designed for OpenCL 1.1 embedded profile in mind whereas I believe the SGX543XT predates OpenCL 1.1.
Personally, I'll be interested see how big the A5 is. The A4 already uses the 45nm process. Samsung's 32nm process was reported as not being ready until closer to the end of 2011. It's hard to see how Apple could fit a dual core A9 CPU with a SGX543 or greater on the same 45nm process without sacrificing battery life. Perhaps they really are going to stick with a single core, but even that should still result is a noticeably bigger die than the A4.