Absolutely not! Where do you see all this hatred? It seems that in recent years, The Wind Waker has been accepted by most of the fanbase as a good game. Nintendo themselves seem to love The Wind Waker -- we wouldn't have The Wind Waker HD if it was an "old shame".
Instead, I think the reason it's not being included is because it's not nearly as popular as the other games. Though hardcore fans know about TWW and like it, it's never been something that the mainstream Zelda audience, those that aren't hardcore fans, really care about. They're comprised instead of the nostalgic Ocarina of Time fans, the modern Twilight Princess fans, and the newer Skyward Sword fans. It makes perfect sense that they're focusing on those three games; they're trying to attract the larger part of the fanbase.
Look at it this way. It's not that they're EXCLUDING The Wind Waker characters, it's that they're determined to INCLUDE the characters from the more popular games first. After all, do you think they view Majora's Mask as an old shame? There aren't necessarily playable characters from that game, either. And what about all the other Zelda games that also aren't being included? (I mean, I'd personally LOVE to see Marin as a character...)