I think part of the problem, aside from the toad, is that stage 2s require so much deck space. Even a 3-1-3 line is a 6th of your deck. With deck space tight enough as it is, most stage 2s are just not practical. That said, I think that with the right build, stage 2s can be put into winning decks.
Machamp/big basics has always been pretty strong. Korrina for Rare Candy and Machamp makes it so much more easier to get Machamp out. If the toad comes out, Hawlucha can take care of it and the deck can still hold it's own without Machamp.
Stoutland is another one that I have had great luck with. It has a decent attack and an absolutely devestating ability (so much depends on supporters). Like with the Machamp example above, I made sure not to depend on it so I used some already strong Pokemon (Yveltal/Yveltal EX/Darkrai EX) as backup.
Crobat from Phantom Forces is another one I noticed popping into decks. It's splashable, it snipes, and most importantly, it doesn't need rare candy as Golbat is pretty good too.
Outside of that, I'm not sure.
-Dive Ball makes water Pokemon more playable. Blastoise sounds good in theory, and if you use Pokemon that can hold their own without Blastoise (Kyurem EX and Mewtwo EX for exampe), it could work. I also faced an Empoleon/Dusknoir deck and got steamrolled. And while I haven't found the best build for ancient trait Swampert, it is pretty strong once you get it out (could be good with ether for even more acceleration).
-I also see potential with some grass Pokemon since they hit that toad for weakness. Shiftry FF and both Sceptiles from PC could be good (especially with the acceleration from ability Sceptile).
-Lastly, there's stuff like Hydreigon (PHF) and Delphox (XY). Things that teetered on the edge of playability, but could resurface with the help of some more support (teammates and repeat ball).
TLDR: I think stage 2s have a lot to overcome and it's much more practical to use stage 1s and basics, but I think certain builds can succeed if the stage 2s provide enough of an advantage while not causing the deck to fall apart if you can't get them out.
Machamp/big basics has always been pretty strong. Korrina for Rare Candy and Machamp makes it so much more easier to get Machamp out. If the toad comes out, Hawlucha can take care of it and the deck can still hold it's own without Machamp.
Stoutland is another one that I have had great luck with. It has a decent attack and an absolutely devestating ability (so much depends on supporters). Like with the Machamp example above, I made sure not to depend on it so I used some already strong Pokemon (Yveltal/Yveltal EX/Darkrai EX) as backup.
Crobat from Phantom Forces is another one I noticed popping into decks. It's splashable, it snipes, and most importantly, it doesn't need rare candy as Golbat is pretty good too.
Outside of that, I'm not sure.
-Dive Ball makes water Pokemon more playable. Blastoise sounds good in theory, and if you use Pokemon that can hold their own without Blastoise (Kyurem EX and Mewtwo EX for exampe), it could work. I also faced an Empoleon/Dusknoir deck and got steamrolled. And while I haven't found the best build for ancient trait Swampert, it is pretty strong once you get it out (could be good with ether for even more acceleration).
-I also see potential with some grass Pokemon since they hit that toad for weakness. Shiftry FF and both Sceptiles from PC could be good (especially with the acceleration from ability Sceptile).
-Lastly, there's stuff like Hydreigon (PHF) and Delphox (XY). Things that teetered on the edge of playability, but could resurface with the help of some more support (teammates and repeat ball).
TLDR: I think stage 2s have a lot to overcome and it's much more practical to use stage 1s and basics, but I think certain builds can succeed if the stage 2s provide enough of an advantage while not causing the deck to fall apart if you can't get them out.
