People tend to be picky pricks.
The more options they have to suit their liking, the better, and believe me, that's for the best.
I will give you the clear example I went through before Snes9x 1.54.1 became available (Snes9x).
I had both Snes9x 2010 and standalone Snes9x, why?
Because Snes9x 2010 ran BS Zelda MottZilla's Project without issues, while Snes9x did not, it gave me a black screen with every boot for that game in particular. Remember that by that time, standalone Snes9x was based on version 1.53 of Snes9x, which had some issues with BS games.
Once qwertymodo added support for MSU-1 to the official Snes9x, the Snes9x core got updated to reflect all changes made up to 1.54.1, now making BS Zelda playable.
That is one reason why having options is the best way to go about this, some people prefer Nestopia due to being accuracy whores, and that's okay.
I only care about the game playing, looking and sounding right, that's all.