Fridge Horror: World 2-3's background contains hundreds of Goomba statues. These are memorials of all of the Goombas you killed thus far.
It's the Same, Now It Sucks: The Wii port, released for the 25th Anniversary of SMB1. Mind you, the quality of the port itself is perfect - the beef people had with it was that the game was a full-priced rerelease that basically slapped an unaltered ROM of All-Stars (not even All-Stars + World!) onto a Wii disc with a modest art booklet and soundtrack CD to accompany it, instead of just releasing the game on the Virtual Console for far less money.
Polished Port: All-Stars gave all four games the ability to save as well as improved graphics & sound.
The version of Super Mario World included on SMAS + SMW may also count as a milder case of this due to Luigi being given new sprites that weren't just palette swaps of Mario's.