HELMIC'S PROFILE

Seems there's a game breaking bug when you get to Lavie's grandmother's house. It's possible to trigger the hopping bird animation before you get the quest for it, and then when you do get the quest the chest is no longer there. Really don't want to start a new game.

Flat out asking is a very bad idea. It's very forced, breaks the immersion. I mean, would Meryl's death in the bad ending of the original Metal Gear Solid have nearly the emotional impact if it happened because there was a pop-up prompt asking which ending you wanted?

Perhaps allow for a new game+? After getting the "default" ending, you can get an inventory item that defeats some otherwise unbeatable boss or acts as some sort of quest item. Or perhaps allow extra dialogue or interaction options that assume the player or character already knows something the story hasn't revealed yet, as Pokemaniac suggested.

Since I haven't played Act III yet because I've lost my save data from the first two acts and I want to wait for the Complete Edition, I'll use a more abstract example. Alice sees Bob and has two dialogue options: say hello or wave goodbye. After Alice chooses one of the options, Bob kills her with the knife he had hidden behind his back. On playthrough two, Alice sees Bob again but now has a third option: she can become suspicious and ask Bob what he has behind his back. Bob may or may not kill her after that, but the story thereafter changes. Bob's attack remains a surprise on the first playthrough with no hint that it could be somehow avoided, but on the second playthrough the option is there without requiring a dead squirrel in the player's inventory or some cumbersome password.

Then there's Cave Story's method: it will tempt you to go after the "default" ending by offering upgrades that the player can turn down. The vast majority of players, unless they're using a guide, are going to accept the upgrade. Although Cave Story doesn't make it clear even after finishing the game that those choices had any impact on the story, once the player knows they matter he can go back and get that secret ending, even if he had already deleted his old save data. It doesn't have to be upgrades per se, but it should be something that really, really encourages the "correct" choice the first time around: a reward of some sort with an option to go back and accept it even if you turn it down the first time. Accepting some party member into your party, not knowing that he will betray you. Traveling to some town to complete some objective, not knowing that you'll be trapped there while something dire happens in your absence. Or completing some easy quest not knowing that it actually helps your enemy.

Again, I don't know (or want to know) what happens in Act III, but there has to be SOME alternative to OOCly asking the player what ending he wants. Even if you highly suggest the player select a certain option, you're giving him a big red button and telling him not to push it.