Although the Bottled Fairy makes more sense than the Heart Containers (due to the Fairies solely restoring health, as opposed to the Heart Containers restoring health and increasing maximum hit points/HP), it'll be weird if Heart Containers are outright replaced by Fairies in Bottles... My first glimpse of a Heart Container was in Super Smash Bros. 64, and subsequently in the The Legend of Zelda series proper. I wouldn't mind the Heart Containers staying in All-Star Mode, though.
I don't get the mention of "can even heal fighters who have accumulated 100% damage"; I mean, all healing items can heal fighters who have accumulated 100%+ damage....it may not be complete healing, but it heals something (provided that the damage you sustain during the healing process doesn't exceed the maximum healing amount of the given healing items). >_>
In any case, I hope that the Bottled Fairies heal adequate amounts of damage (preferably more than 50%); it disappointed me in The Legend of Zelda: Twilight Princess that all of the health-restoring Fairies were pretty much outclassed by the more-readily-available Blue Potions...