1) Thunder can still hit a flying target. It also has a chance of breaking through protect if it's raining. Sky Uppercut, Hurricane, Gust, Whirlwind, and Twister can also hit a target.
2) Earthquake will hit the Pokemon and do double damage.
3)Thunder Won't hit a diving Pokemon, however, Surf and whilrpool can. Earthquake or a fire type move won't hit a diving Pokemon either.
Locking moves/abilities like Mind Reader will also do the job.