I have heard some speculation that as these "classic mini" consoles move into the PS1/N64 and forward era that licensing and emulation is playing increasing problems. The NES and SNES have been for all purposes "perfectly" emulated by fans for ages now, let alone Nintendo.
The PS1 and N64 have yet to reach that state with either the fanbase or the companies themselves. Most people forget for example that the PS2's list of PS1 games that "didn't work" with the console increased with every revision of the hardware and certain Slim models can have some serious issues.
Lots was made of the fact that Sony reused the PS1 CPU in the PS2 and while that helped the console was still doing emulation of the GTE on the EE/GS. Games that ignored certain Sony libraries had some of the largest issues. I believe the Slims got rid of the PS1 CPU altogether, and they made revisions to the EE/GS especially after it was made a single chip. This caused backwards compability issues with PS2 titles, the media didn't much care about PS1 backwards compability at that point but it also took hits from this. Even fewer people paid attention to the PS3's situation on this.
I believe Sony's PS1 emulator has been derived from the PSP version they created since they had to emulate everything finally. Much like Dolphin, where you can get better results running the VC versions of N64 games through it than through N64 specific emulators, PSPPP shows similar results running PS1 classics. (I think I saw one of the knowledgeable GAFfers recommend emulating that version of Symphony of the Night over using a PS1 emulator.)
Rainbow Six continues to be the most baffling inclusion of all unless it's some kind of UbiSoft representation thing. If/when the N64 mini comes out the first thing I'm looking for is that console's crappy Rainbow Six port alongside Rayman 2.