Well, I disagree with you.
Every single time Nintendo has gotten the worst versions of a third party game, it was because of hardware limitations. Third parties don't just say "Oh it's Nintendo. Let's give them the worst version of our games".
In that case Nintendo owners must be lucky because their platforms do not often get the worst version of any given multi-platform game.
N64 got the worst versions of Resident Evil 2 and Megaman legends because it used cartridges over CD's.
Nintendo 64 has the best versions of Resident Evil 2 and Megaman Legends. (The cartridge-based storage medium improves loading times but otherwise doesn't really come into it.)
GameCube got kind of screwed because it had smaller disk space than normal DVD's. Although many third party games did look better on cube than ps2. Cube also had no online.
Less storage equalled slightly more compression artifacts in full motion video. Other than that Gamecube had the best traditional gamepad ever making for a much more immersive gaming experience than its competition. (The same could be said for Wii as regards its control system.) The reason Nintendo did not get as many third-party releases had everything to do with Microsoft and Sony partially 'sponsoring' development and/or marketing on just about all third-party releases, which was up until relatively recently something Nintendo refused to do to any great extant.
And Ps2 on-line was barely more used than Gamecube on-line.
Wii got worst versions because the graphics were crap and it had crappy online and no harddrive.
Many multi-format games have their best version on Wii. A few examples include Bully, Dead Space: Extraction, Ghostbusters, The Godfather, Goldeneye, The House of the Dead: Overkill, No More Heroes, Overlord: Dark Legend (>>>>> Overlord 2), Sonic Unleashed, Star Wars: The Force Unleashed 1 & 2, etc.
Heck, I'd even be willing to throw Call of Duty: Black Ops in there - less players per map make for a more tactical experience, the removal of certain killstreaks improve the play balance, and the superior controls take the game to a whole new level of immersiveness. And it's the best Call of Duty to boot.
In every single instance, it was not the third parties giving Nintendo the worst version of a game just because it's Nintendo. They got the worst version of the game cause their systems always have one limitation or another.
To reiterate, Nintendo do not often get the worst version of a game. But when they do, the limitation you mention may more often be found with the abilities of the third-party than those of Nintendo.
