I feel if you're going to make a direct sequel to a game with multiple endings, it should be based on the ending that makes it the most compelling. Metal Gear cheated and basically told us the true ending to MGS1 was a variation incorporating both endings to the game.

I know in SMT2, its a direct sequel to the first game, incorporates the "Neutral" ending as the true ending. There's also Suikoden III where you get to choose the lead character and sadly, the biggest drip of the three is the canonical lead character according to the books. Just to name a few more examples.

Personally, I feel you should incorporate the best ending to make a compelling sequel. Sometimes the "good" ending is there solely for the people who absolutely need a happy ending. But this is just my thoughts.