I know I only play the GBU metagame and things are slightly different, but I never have too much trouble with Thundurus. It usually needs to OHKO the opposition, and if it doesn't, it likely dies unless it's just getting walled/stalled. I don't run into Substituting sets often, but if you don't let it set up a Sub, there's not much to worry about.
Also, for a "counter", there's Lanturn. GK has a weak BP because of Lanturn's light weight, while nothing else Thundurus can use can deal too much to it (unless it gets lucky with Focus Blast).
Edit: Oh, about Drizzle: Maybe it's just GBU, but it's really not that threatening. Chansey/Blissey (I prefer my Snatch Bliss over my Minimize Chansey most of the time, so I can Snatch Kingdra's Subs and such) pretty much wall everything that can abuse rain (with the exception of mixed Thundurus/Tornadus and Toxicroak, and UU Pokés like Swift Swim Poliwrath).
Also, for a "counter", there's Lanturn. GK has a weak BP because of Lanturn's light weight, while nothing else Thundurus can use can deal too much to it (unless it gets lucky with Focus Blast).
Edit: Oh, about Drizzle: Maybe it's just GBU, but it's really not that threatening. Chansey/Blissey (I prefer my Snatch Bliss over my Minimize Chansey most of the time, so I can Snatch Kingdra's Subs and such) pretty much wall everything that can abuse rain (with the exception of mixed Thundurus/Tornadus and Toxicroak, and UU Pokés like Swift Swim Poliwrath).