I'm not going to say that I didn't like Lyra, but I kind of like Kris a bit more. But that's also me speaking from the fact that I played Pokémon Crystal back in the day, so that's what I'm used to.
That being said...
The name of the games are also Pokémon Heart Gold and Soul Silver, nothing about Crystal. The original Gold and Silver did not have a female player, therefore, GameFreak probably felt the need to create one instead of using Kris...though it probably would have made more sense using Kris as she was an already established character. I don't know. If I had the chance to, I'd ask, but unfortunately I probably won't ever get that chance. lol