She's basically an insert from the Tecmo Koei team, but also, the only main series game to ever include characters from a previous title was Majora's Mask. For the rest, while some characters were familiar (Link & Zelda among others, obviously), they were always in a vastly different time. Lana is an anomaly even in Hyrule Warriors because she's just an offshoot from a sorceress that's able to see into other worlds. If they were to put Lana into a main game there would also have to be a Cia, possibly along with direct references to or even character appearances from other games.
While the series definitely needs something fresh (and HW is a great point to start off from), I think those story rules are so ingrained into the franchise that Aonuma would be skeptical about having them changed at this point.