Hmmm, Having thought about this for a while, I thought I might chip in my personal solution;
Buy the right to use an existing GPU, Nvidia Geforce or ATI radeon (it doesn't really matter which).
Then design you own board, this is important, as you need to select a powerful DSP and give it access to the GPU's registers, also give the DSP some memory of it's own (2Meg anyone?). In that memory map an emulation of the AGA registers. Now let the DSP run an AGA Emulation controling the GPU.
This way you have full access to the modern GPU, but also all the features of AGA in hardware (which can be updated via a FlashROM on the card).
Other than the Copper (which I miss), I'm not really sure what features of AGA are usefull in a modern world. The DSP's main function would be very similar to the Copper in the AGA chipset.
