I'm not opposed to an emulation based implimentation, so long as it is indistinguishable from a hardware based one. If we are talking about making a dedicated 2600 clone with the core chipset running in emulation on a microcontroler, vs having it implimented with an FPGA, There are several things that both would have in common. For example both would need a custom PCB, cartridge connector, controler ports, switches, and a case. I favor designing new controlers to put the console switches on the controler. I also would want to have some circuit that takes the TIA output and processes it to work better with modern displays.
The question then is, how hard would this be?
For the emulation version, you would have to port Stella to whatever microcontroler is chosen, and make it work better than it does now on Windows or Mac. For the FPGA version, you would need to port over the VCS chipset to Verilog or VHDL, and make it work better then the Flashback 2 works. I don't have the experience to state which one would be harder, but there is at least one person who has gone the FPGA route:
http://tolgaretro.blogspot.com/2007/05/atari-2600-on-fpga.html
It looks like he etched his own board, too. He used a 100,000 gate FPGA and as far as I can tell, it was about a $9.50 part.