I don't find the wild pokémon too obnoxious. They are quite challenging at times but what annoys me more is the random trainer encounters once you beat them the first time you have to fight their level 40+ pokémon with you ~level 12 pokémon which logically result in you beeing defeated and losing money and happyness.
For me that is the bigger issue. Maybe the forced trainer encounters should be separated from the regular ones and should have pokémon levels that at least somewhat match your own pokémons level.