We saw the beginnings of this trend last generation: Splinter Cell (exclusives map on PS2, GBA connection on GameCube), Soul Calibur II (platform-exclusive characters), and Prince of Persia: Sands of Time (original Prince of Persia emulated on the PlayStation 2, the sequel Prince of Persia 2 on the Xbox). It will only get worse this generation.
It used to be that you could buy all three platforms and the exclusive games for each. Now, to get access to everything you not only need all three platforms but also all three versions of a particular game. Lovely.
And, yes, I did buy both versions of Pinball Hall of Fame, one for my PlayStation 2 and one for my PSP.
Go back two generations for something similar, though not quite the same.
Capcom openly favored the Saturn over the PS1 for 2D games. In addition to arcade ports being superior on the Saturn, Capcom added extras to some of their multiplatform Saturn games.
SNK took the opposite path with their arcade games. Inferior PS1 versions received extras.
And yo don't have to go just to consoles, as from various reports, "extra features" are a requirement to release a multi-platform game onto the PSP. (It has been mentioned in regards to both X-Men Legends 2 and Viewtiful Joe: Red Hot Rumble.)
Mentioning Soul Calibur II is interesting, considering Soul Calibur 3 was platform-exclusive. And a true one, not just a time-restricted exclusive.
I believe that Madden, Special Edition was PS2-specific (with the PS1 and Genesis versions included with slightly updated rosters).
Still, with this and baines' comment, I believe you've still arguably got at least one "superset version." I believe his -- creative and original -- argument is that you'd have to buy, in the case of SNK, two versions to get both the hidden goodies *and* the best version of the games, but, as someone who played through TR exclusively on Saturn (sounds like I'm shilling), as long as the game's all there, I believe any one's fine.
Otherwise you might argue that an N64 version of a game is inferior because of sound and a PS1 version of that game inferior for load times, etc. Approaches the ludicrous, taken outside of baines' hand-picked (and more representative) selections.
(Course you can't really say you've played TR2 unless Lara was obviously using a Powerbook with an Apple on the cover.)
And yo don't have to go just to consoles
I was really hoping this was some veiled reference to Parappa (the driving song). Still looking for the how, though.
Capcom didn't necessarily favor the Saturn, it was just a stronger machine for 2-d.
As for SNK, you are way off base. SNK made arcade-perfect Saturn versions of many of its fighting games, they were just never released outside of Japan, due to Sega's bonehead play of never bringing the memory expansion carts out in the North American market.
Oh, by the way, every Saturn Capcom fighting game from Marvel Super Heroes onward used the memory expansions. Oddly, MSH ran better without the expansion, as the reduced animation was fars smoother than the full animation coming through the memory cart.
If they had made it require the expansion, it would have been perfect, too.