If you have one (or more) different endings for a fic in mind, it's not that big of a deal. You can pick one for the main fic and then write an alternate ending as a separate fic. Just a fun little bonus!
But what the heck do you do when you have too many different ideas to *start* the fic? An alternate beginning changes the entire trajectory of the story, so you'd just have to write two whole-ass fics. But wouldn't it be silly to have two of a very similar story? Guess I'll just have to.... decide! :V (Looking at YOU, Garrison au!)
On a related note, I think it would be fun to do a "choose your own adventure" type format with one of my fic ideas sometime. That or just have an ask blog-esque thing where people can affect the plot through asks/polls. I didn't want to do something like that initially because I was worried I'd get discouraged from lack of interest. But I think I have enough material for ideas that I could move things along even with super minimal engagement. Sooo... Maybe! I'm thinking Garrison au, Second Chance au, or maybe even Sails' Tales (Someplace-Sails' backstory) for that format. Maaaaybe even the Folklore au once a certain point in the story is reached. Speaking of alternate endings... heh.