This is just my opinion (and I'm not very well versed in things like processors, etc); but comparing two phones' speeds via speed tests is sometimes a tricky process. Slap two phones together and see which one is faster - I did this with two flagships I wanted; and it certainly left me with a disappointed impression of a particular device, like in your case.
I guess what I'm trying to say is, both the Honor 9 and the LG G6 have good specs and run well based on those specs. If they have fairly new processors or at least the most recent ones, then they are expected to operate in a quicker manner. Perhaps you wouldn't have noticed this "lack of smoothness" with the Honor 9 had you not been testing the two.
We want to test because we want to know which phone is best for us... But then these things happen and we are sad. I feel your pain!
My advice to you is to go back to the store and fiddle around with the Honor 9. It sounds like you were wanting to enjoy it - see how it fares on its own and go from there. And, of course, keep us updated on what you decide to get!
PS: The G6 and Honor 9 are on my wishlist, too!