Link was originally played by someone else (the voice at the end of Season 1) but he was unavailable for Season 2.
Christian (Ryu) could've played Kid Icarus in Season 2
Julian (Snake) was a big fan of Resident Evil 4 and wanted to be Leon in the show.
Dane was given the option of playing Ness or Ash. He chose Ash cause he loved Pokémon.
Richard (Mario and co-creator) during Season 1 almost wrote several episodes that took place before Mario's very first trip to the Mushroom Kingdom, where he was a normal teenager working part time at a plumbing company, and where Merlin opens the portal to the Mushroom Kingdom and gives him his hat. However he and Chris (Luigi and co-creator) decided that is was too much backstory for a comedy show.
Word of Saint Paul: Kevin Chamberlain (Yoshi) owns a youtube account here where he often does a series called History of Stupid Mario Brothers (inspired by Linkara'sHistory of Power Rangers) which shows his own opinion on the show and confirms several things in real life that Richie hasn't.
The creators and actors tend to go on the Fan Forums to answer fan's questions. A fan should be warned they don't go on as much as they used to, although Season 4 has already contained characters suggested by fans and fans had bombarded them with villains for Season 5. With Season 5 over they've been a bit more active reading fan's reactions and input.