Weaknesses, just brief what comes to mind.
Trick leads - Alakazam, Azelf, Persian etc
General Scarf leads - Dragonite
Faster taunt leads - Aero = pwned by icebeam, Weavile
Locked into Hp water - Breloom, gyarados, Salamence, dragonite, Metagtross Any_water_type_w/_Ice beam
Locked into energy ball - Heatran, Infernape, Blissey, Celeb, Gyarados, Salamence, dragonite, | fire/steel/grass types in general
Locked into Leaf Storm - Same as above
Locked into Focus Blast - Gengar, Rotom, Dusknoir, Gyarados, possibly salamence, but I'm not sure how much it would hurt it, same with dragonite
Blissey, Gliscor (outspeeds and OHKO's this set w/ EQ), infernape, gyarados, scizor can hurt, flygon
Any late game taunters such as gyardos, hazers and phazers such as swampert, skarmory, weezing, suicune. Walled by spiritomb.
If you don't keep this is for more than a turn or two, then this thing shouldn't have any weakness. You want fire blast on the set as Flygon needs all the power it can get. However:
Locked into EQ any levitaters - Gengar, gyarados, azelf, salamence, dragonite, flygon, rotom etc etc.
Locked into outrage Vaporeon, suicune, gliscor, forretress, metagross, steelix, skarmory.
Locked into Fire Blast Heatran, suicune, blissey.
Those are my blatently obvious weaknesses that I can see. However your team should have most of them covered. Bulky waters and gyarados look Like they may pose threats, so if you can allocate a move for hp electric/thunderbolt/_electric attack_ then cool. However seeing as most bulky waters attack from the special side, and seeing as swampert won't hurt blissey too much, toxic stalling should remove those problems.
I'm too tired to tell you how you counter those weaknesses, but in looking at ways you think you can counter them, you should devise a better strategy.