Secret Endings like that are just typical pitfalls for completionists. It's supposed to be an optional reward for the people who voluntarily spend all that time on the game. But in the eyes of some players that "optional reward" becomes mandatory cause they want to get everything out of the game they paid for and so they spend hours upon hours on a game they don't even enjoy (that much). Basically going completely against the thought process that put the scene in there to begin with. It's not really supposed to be something to work towards, it's supposed to be a nice surprise at the end of the road. FFX-2 suffered from the same problem.

I feel the way they handled Alyssa's story was okay. It's not relevant past the betrayal because that's when you - and the protagonists - are straight up thrust into the final part of the game and don't really have the time to think back on it. But if you really want to know, all the pieces of the puzzle are there, you just need to put them together.