Jirachi: Water Pulse/Thunder/Sub/CM Variants, although rare, spell doom for me. As long as they keep rain up, he can keep on setting up and just eat me alive. Very tricky to deal with.
Volcarona: If Tyranitar goes down, I don't have much that can stop a boosted Volcarona bar wearing it down slowly with Bullet Punch from Scizor or hoping Rotom-W is faster. This is the original reason why I kept Heatran over Celebi originally, but using Heatran opened up a bigger weakness to the above Jirachi and rain teams in general.
Politoed: More of an annoyance that an actual threat; the reason why I had to use Celebi over Heatran for more consistency due to how popular Rain teams are. Depending on the set, I can play around with it to deal with it accordingly; Tyranitar can tank a Scald from bulky variants and hopefully not get burnt, 2HKOing at best with Stone Miss. More offensive variants have to be played with more carefully; I NEED sand up for Tyranitar to stand up against Specstoads.
Dragonite: Hurricane variants are handled by Latias decently well, but the standard set is a pain to deal with. I need to get SR up no matter what, or I will have to rely on Rotom-W to KO it; even then, with Dragonite's natural bulk, it's shaky and I have to end up sacrificing 2 Pokemon just to take one down... if it dosen't completely destroy me first.
Landorus: Scarved or Banded ones have to be locked into the wrong move at the wrong time to go down easily, but LO and Expert Belt variants are a little tougher to handle. Latias can take a HP Ice with more than enough to spare to Recover and continue setting up CM, but if Latias is weakened beforehand it spells my defeat pretty easily.