Hello Althah!
Alirght now lets start.
1st Endure my bad english for the next few minutes while you read my post
With one view your team is pretty decent and you can counter almost every type expect fairys i think only your Rhyperior can but i dont think that he is fast enough to do the first hit and that makes him kinda weak anyway.
About your Rhyperior you could change him for an Aggron (as you said) but sadly earthquake isnt availble yet,Some another choices are Flygon and Nidoking if you want.
For your Milotic well i think that depends on your Milotic's IVs if he have beast IVs keep him if not well change him and try to learn the Ice Beam and Scald by breed (tbh i dont really know... i think he cant learn any of these http://bulbapedia.bulbagarden.net/wiki/Milotic_(Pokemon) use it the link on googlechrome).If you really want to replace him you could use Lapras instead (HYPE! ).
Well for your Honchkrow tbh i dont really know whats going on there since my Murkrow have Bravebird from the start probably the moves are rng so if you want you can breed him with a ditto or change with Gliscor or Archeops as you said.
Finally for your last Question your Heliolisk can learn Hyper Voice from toturing the only trainers atm on the game are on The 7th street and on Circus if i am not wrong so if you cant find your move there then isnt availble yet.
I am really sorry but i cant answer on your rest of your questions because i dont really know whats gonna happen on the next episode i mean on what items we gonna have access .
Alringht now i am gonna post my current team if you want go ahead and check if you want to get some ideas