Dave,
I run my new Legacy GP-9 with the LionChief app and Universal Remote. It's my first Legacy engine. Trouble is, I don't have the Legacy system so I can't tell you what I'm missing. For now, it behaves like a my LC+ engines albeit with nicer sounds. I'll be taking delivery of a Legacy system soon.
I'm told that I will be able to control my Remote/Command FasTrack switches via the Legacy remote. If that's true, then that is one difference right there. By the way, while I prefer the Universal remote, the one thing I like about the app is the ability to turn off smoke. If the Universal remote had that capability, I'd never use the app.