I though you shouldn't use Secret Power because that move is not too strong. For your Rapidash, remembered Poison Jab and Horn Attack it will raises your Rapidash's attack more powerful. For Milotic, you shouldn't use HM waterfall, that move isn't too strong. Your Togekiss... No comments! That moves is powerful! For Salamence, don't use Dragon moves more than one, forget dragon claw and try other moves from using heartscale or TM's. And Dragonite, forget dragon claw and thunderbolt, replaced that moves for shock wave and other TM's, why? Because if your Dragonite confused by pokemon water type's supersonic or confuse ray you not too able to use thunderbolt. That's all!
Your team is awesome. But I think that you should give Rapidash more powerful instead of stomp.You can replace with ground type move or other normal move that is stronger than stomp. For normal attack, I really like body slam, but I don't know whether Rapidash can learn body slam.