PPSSPP and Dolphin have made great progress BECAUSE they were open.
long story short, it is the real solution, but its not a practical one by any means.
The hard part is for someone to actually develop the emulation for all the custom chips in the system. In particular, the two graphics chips are very complex and the documentation is very hard to understand. The same goes for the sound chip. The others are all standard enough to be reasonably straightforward (if not actually easy).
Here are some relevant links (I'm sure there will be other systems that have been recreated in FPGA form):
http://www.retrocollect.com/News/super-nintendo-recreated-in...
http://hackaday.com/2013/01/23/stuffing-an-nes-into-an-fpga/
http://www.sega-16.com/forum/showthread.php?12847-fpgagen-a-...
Emulation is the best possible path IMHO since it enables the games to be played (and experienced) on pretty much any hardware. I think this work may do quite a bit to help in that area, there's really no reason the Saturn isn't nearly perfectly emulated these days.
Reproduction is the next best and much harder than Emulation. Basically figuring out how to build the hardware again. There's several versions of this with much older hardware (C64, 2600, etc.) with new hardware being produced that can run the old software natively. There's also "lesser" versions that use modern CPUs, etc. to run the code basically also in emulation, but this is not the same thing. However, reproduction is both technically more difficult and has a smaller audience who's willing to add yet another machine to their collection to see old games.
also, MESS's emulation is also not too terrible, I was pretty surprised with how many games worked under it
In a hundred years, the only practical way to experience classic software like this will be via emulation and I believe that's where resources should be put.
There's a weird kind of snobbery in classic gaming that, unless you're playing original games on original hardware, you're doing it entirely wrong and emulation stuff is basically just dirty piracy. Fast forward to today and the talk of the community is that old game and hardware prices are getting sky high, and in the case of some systems (like the 5200) finding working equipment is getting to be impossible. No duh, sucking all of the inventory for a product that's not going to be manufactured in anymore and allowing the prices to slip into normal supply-demand areas means that's what's going to happen -- even worse, the new audience who can be exposed to this material shrinks even smaller every day.
For almost all practical purposes, systems like the Amiga or the SNES or similar vintage are pretty much complete in terms of emulation -- the entire known software libraries are basically completable. In many ways, emulators like UAE offer better software compatibility than real hardware!