It looks like there's going to be more to Hyrule Warriors Legends on 3DS than meets the eye, if this Famitsu interview with producer Yosuke Hayashi is any indication. Apparently the inspiration for a portable version is literally as simple as Zelda fans noting that they wanted to take it on the go, so the team started development to meet that demand.
Evidently Wind Waker content was cut from the original release because "it wouldn't work with the story," but with the new 3DS game, they had a chance to create an epilogue-like situation that did allow it to work. The Wind Waker portion will actually continue the core story and won't be fluff. There will also be StreetPass support for Adventure Mode, a spring 2016 release target, and amiibo support that will be similar to Wii U.
As for other new content, the King of Hyrule and Tetra have been confirmed already, but Hayashi notes that "we plan to add new characters other than [those two]. There are fan favorites...so I'd be happy if you kept guessing who will join the fight while waiting for follow-up information."
Well, Agahnim is basically a shoo-in at this point right?