This team is overall very solid and it uses some original sets, which is pretty cool, but as you have outlined, it has some weaknesses that need to be ironed out. The first problem, that you have already noticed, are some special threats like Roserade, Chandelure and Raikou/Zapdos too, as Rhyperior can't reliably stop them with an offensive spread. I also feel that Meloetta isn't doing much for your team and ''it's just there'', so I would recommend using Choice Band Snorlax instead, as it lets you handle Chandelure and Roserade a bit better while still being a good offensive pokemon. Set:
Snorlax@Leftovers | Thick Fat
Adamant Nature | 252 Atk / 252 SpD / 4 Spe
Return / Earthquake / Crunch / Pursuit
Using Return or Body Slam is up to your preference, and I guess you could also use Leftovers on Snorlax but yeah, that's up to you!
The other problem this team has is dealing with Sableye. There isn't much that can be done to solve this without changing the team a lot, but you could try using Shaymin (or Roserade, but it isn't as bulky and can't check Kingdra) instead of Rotom-C. Shaymin has the advantage of having Natural Cure, and being able to run an offensive set / spread while retaining the necessary bulk to switch into Kingdra and other water type pokemon well, and it also has a recovery move on Synthesis or Rest.
Shaymin@Life Orb | Natural Cure
Timid Nature | 252 SpA / 4 SDef / 252 Spe
Seed Flare / Earth Power / Psychic / Rest | Synthesis
Hope I helped!