magnezone absolutely destroyed Skyla, they should have given her a gliscor or something.
I don't think I've ever had trouble with a gym leader except maybe Brock when I picked Charmander as my starter way back when. Skyla and all the rest pretty much get OHKO sweeped by one or two of my best Pokemon.
I don't know if challenge mode is different, but keeping one or two fast sweepers with wide coverage basically lets you dominate every Pokemon game so far. Unless you are a beginner, I find it hard to believe that any gym leader would create much difficulty outside of intentionally crippling yourself (not using any previously fainted Pokemon, running from/avoiding all wild battles and avoidable trainers, using a specific team of weak or unevolved Pokemon, etc).
I just got to Opelucid, but am going to catch a few missing Pokemon before I take on the gym leader. So far I've missed the Dunsparce, the -sage trio, Seviper, Zangoose, Durant, and Onix. I catch those and I will have all the Pokemon I've encountered in-game so far, at least for the season (but none of them seem to be showing up...). Pokedex sitting at 201 right now.