If you want to do it, then the best idea is probably to build the whole thing (CPU and all) in an FPGA, with a simple RF tuner + some DACs + a rom (witha kickstart + a simple workbench and ADF loader). Then have a CF or SD slot for ADFs.
FPGA is one way but there are also psudo-custom chips which are existing systems with a customisable block.
Another way might be to use one of the new multicore embedded CPUs (20+ cores per chip), it takes a lot of power to do a good emulation of the chip set so you could break up UAE and run bits of it on each core, it may then be fast enough to run it in software.
Multi-core may not work that well though and requires additional components anyway - and has GPL issues...
Wouldn't be cheap though.
If you wanted to produce a system like this it's going to be expensive anyway, you can't make them cheap to sell unless you produce them in fairly serious volumes and we're talking $2 million + for a 100K unit production run (assuming it's $20 to produce).
Even if you spent $2 millon on chip development that's another $20 per unit but that assumes this would be the only production run.
I think the best way wold be to take an existing System on Chip and modify it to include the Amiga chip set (or parts thereof) as a module, this'll produce modern device with Amiga compatibility.
It's no small undertaking and definately not cheap but there's no reason that it can't be done.