>>28592945More in gyms have 6 pokemons each that cover weaknesses well. The pokemon distribution according to areas is in a way the good pokemon are harder to obtain, making you use mons like Swoobat for example in some occasions.
Game also incorporate field effects, so you have to have knowledge of them, wihch becomes crucial later on. Like, say, if you are in an area of the game that is polluted, a battle in such are would have Poison Mist as a field, which benefits poison pokemon, but you can use moves like Gust to dispell the mist, or use Fire-type attacks to cause a combustion.
It isn't one single thing that makes it difficult, but many. You may have an easy time, but as if progresses, so does the difficulty. Ghost gym in Rebon for example, is pretty hard.
