@Blusasuke
Have you read Mahoraba? It also involved multiple personalities (in this case a total of five including main) with at least one or a few of one of your suggested endings. I generally consider that story a happy ending. Bittersweet endings are like Shishunki Bittersweet (ending 1)
Radiata Stories, various Kingdom Hearts games, various Star Ocean games, various Tales of games... probably need to add Gakkou Gurashi to this list soon -_-. It is where stuff are generally "not happy" such as someone meeting a tragic end/ not saved/ remain unhappy. It usually gives me a very VERY bad aftertaste. Since this involves multiple personalities my guesses are mostly like yours (fused personality, deaths, memory loss, etc) minus any "successful love stories" like being able to pick who goes away and then successfully getting the other personality.
Its really that or we meet new and more lovable characters that were created to suffer.