The reason why Hypno is not used anymore is simply because while it's sp def was passable in the old UU, in the new UU the special attackers just hit too hard and Hypno's typing doesn't really let him resist much. The good news is that since everybody is all worried about Raikou and Shaymin, they all opt to use registeel and regice, which are completely raped by Fire pokes.
I actually haven't seen that many Regice recently, but yeah, teams that use them do have to make sure Fighting and Fire moves are covered thoroughly elsewhere. My current team uses Lanturn and Altaria as a primary means of dealing with those threats, so that problem is automatically covered for me.
The thing I struggle to understand is why people think Registeel is such a good counter to Shaymin. Most are 3HKO'd by LO Earth Power, whilst unlike Skymin it has great bulk, is not raped by Ice Punch and is not permanently crippled by Thunder Wave.
Ironically, the team I'm using at the moment uses a Reflect / Rest Raikou and LO Cleric Shaymin, which both beat Registeel quite comfortably (apparently on Shoddy critical hits don't ignore the screens, though I'm not sure that is how they're supposed to work). Some counter.
It seems like shaymin is a problem, has Muk been a decent check? Im gonna try him and see.
Well it can work as a check with its powerful STAB Poison moves, but repeated Earth Powers hurt, so I wouldn't rely on it as a counter. But you probably knew that already.