Well, let's...
Cloud is a third party character from a third party company (Square Enix) and he's the poster boy of the Final Fantasy franchise.
Third party characters have different criteria from being included. Final Fantasy VII did leave an impact on RPGs so that probably contributed to his inclusion.
Although the Final Fantasy series has history with Nintendo, Cloud and Final Fantasy VII, not so much. That game was exclusive to PS1 and with the remake coming around, PS4 and maybe even Xbox One despite the nonexistent install base in Japan. Could it appear on Wii U or NX? Who knows.
If there were people who wanted a Final Fantasy character, they were probably thinking of someone from FF1 - FF6 like Cecil or Terra. Games that debuted on a Nintendo console
If there were people who wanted a Square Enix character, they were probably thinking of someone like Geno from Super Mario RPG or Sora from Kingdom Hearts.
Of course, some of these salty people probably wanted someone like King K Rool, Inklings, Isaac, Wolf, Shovel Knight or [INSERT FAVORITE CHARACTER HERE]. If these people expected a character from the Ballot, they're probably acting all paranoid thinking that Cloud won the Ballot.