see this is how the atari cougar could be built, it could play all the systems.. PLUS we some how modify it to have greater memory expansion and things such as MYIDE and sio 2 usb.. and the like..
A bigger memory is fine, because that can be 100% compatible with a 64KB base memory.
All the other extra's: I think it is better not to implent those by default.
If there will be a remake of the atari 8bit line, in my opinion it is the best idea to keep that new one as close as possible to the original. That means: with a SIO port, with a parallel bus (or cartridge + eci) and with two controler ports.
That would be awesome.
Many add-ons do have a few benefits. But there are also counterparts. MyIDE is great (I'm really a big fan of that small interface), but it is one of the less compatible atari 8bit IDE interfaces around.
When the 'new born' atari 8bit does have the 'usual' ports, it is much easier to use your own beloved interfaces and devices again.
One other question:
Who needs a new atari 8bit? I've stored over 70 atari 8bit computers. And some of them are brandnew. I know: they won't last forever, but for the next 10-20 years I'm rather sure I'll have lots of fun with them. They are still easy to obtain here in The Netherlands. And not only here.
Ok... when all those existing atari 8bits are 'dead' ... a remake with new components would be very cool indeed. And when there will atari 8bit available for buying, I would certainly buy one or two. But I think it would still feel like running an emulator, even when it is NOT emulation.