Okay,
So I have done a lot of thinking on this... I ended up keeping Magnezone on the team. He really has been a key player for me all the way back to right before Shade and his flash cannon is just too good to pass up. That being said, he is set in stone.
Jynx, I have been on the fence with. Her special attack is decent and she has pretty good speed. I did however find Sneasel, and Weavile is my favorite Pokemon... So I am thinking I will end up utilizing Weavile as my Ice mon (helps with the dragons and flyers, plus the dark typing will help against psychic and ghost). Also because of the Dark typing I would rather not go for Krookodile.
In regards to being weak against fighting, my Aerodactyl (which I already subbed in) pretty much one shots any of them with Fly. Its a Jolly nature too, so far nothing has been able to outspeed it.
One thing though that I have noticed is that my team is short on special attackers, aside from Magnezone... I am having a really hard time picking one that I like. Chandelure is a fantastic option, but I see a lot of people running them on their team, friends of mine included, and I would love to try something a little different. I was thinking perhaps Roserade? I would get the poison typing with it and the ability to use moves like dazzling gleam, toxic spikes, and leech seed.
All of that being said, I will say I think it will be a challenge to not have a solid fire type pokemon on the team. I am currently stuck at the Titania fight and having a fire pokemon would really really help with this. I may just keep Rapidash in rotation, but not on the main team? How often are fire types useful after Titania?