Hi there. This is a very solid team, and congrats on the peak. However, there are a few weaknesses.
As you have pointed out, full-stall teams are very problematic for your team. Shaymin is your only real wall breaker, and is completely shut-down by Roserade, the most common stall spiker. Rain teams can pose somewhat of a problem, however you have a decent answer to them in the form of shaymin, which can seriously weaken Kingdra, and Rhyperior deals with Tornadus very nicely, bar Grass Knot.
To help with the stall issue, I recommen that you run a Choice Spec Slowbro over Blastoise. Blastoise ruins all of your momentum, and you don't actually need a spinner, since Crobat gets multiple opportunities to Roost up on the likes of Heracross and Scrafty, whereas Houndoom is used as revenge killer to dangerous threats and as a Chandelure / Cofagrigus switch in, and therefore doesn't particularly mind that it's health is being sapped away.
Slowbro is an excellent weapon against stall teams, since it has an answer to nearly every single pokemon on a stall team. Specs Psyshock deals huge damage to Roserade and Snorlax, and break down everything that walls Shaymin. Trick is also a nice move to have against stall, although Grass Knot can be used to lure in opposing Slowbro and basically destroy them. Specs Slowbro also stops Zapdos from coming in for free, as Surf hits Zapdos for a ton of damage. On top of all this ridiculous power, Slowbro can still perform the task of bulky water very well, tanking hits from Darmanitan, Arcanine and Victini with relative ease.
Here is the Slowbro set:
Hope I helped and GL with the team.