I always thought that Wind Waker (combined with Ocarina of Time, Twilight Princess, and Skyward Sword) are the Zelda titles that Nintendo themselves to be the most proud of. Focusing on Wind Waker, it has gained a lot of love throughout the years. It's art style is used for other titles within the franchise (Minish Cap, Phantom Hourglass, Spirit Tracks, Four Swords, and Four Swords Adventures), Toon Link not only appeared as a newcomer for Super Smash Bros. Brawl, but is a returning veteran for Super Smash Bros. for Wii U/Nintendo 3DS and was the second Zelda character to be confirmed nonetheles. Of course, The Wind Waker received an HD remake this past year and was also available as part of the Zelda TWWHD Wii U bundle. I don't think Nintendo considers Wind Waker to be an old shame as Eiji Aonuma stated that Wind Waker is his favorite game not to mention considers the character King Hyrule as a sort of son or virtual image of himself.
Sure it's great to see the Wind Waker (I'm still perplexed to way they called it the Baton) in the game as a weapon that Zelda can use, but outside of that, there is no other form of representation for Wind Waker. There are many characters that they can choose from: Tetra, Medli, Komali, Makar, and even King Daphnes could very well be potential characters that could have been chosen to be part of the roster. For those that don't believe that Wind Waker characters would feel out of place, consider this: Beedle is in Skyward Sword and retains his features and characteristics from the Wind Waker yet has been altered to match the style of Skyward Sword. I don't think it is that much of a stress to see the characters I stated above to be in the game. Really all that need to be done is adjust their models to fit alongside the models that Hyrule Warriors are using. To this day, I am still clinging on to the hope that there will be a character from Wind Waker that will be a playable, specifically Makar as he's one of my favorite character from Wind Waker.