I realize this is a bit of a necro thread. But I feel there is still relevance to this.
While I myself do not mind challenging battles (in fact, I prefer them), I do have a problem with the trainers constantly switching in and out pokemon. A lot of the time it doesn't even make sense and work to my advantage. But the main problem I have with it is that it makes it near impossible to reliably level a weak pokemon early game (for example Magikarp). And since we do not get exp share until much later this becomes a prominent issue. If temporary. It is however, a problem.
Please consider balancing this, at least for the early game encounters as at this point it wont really add any difficulty but is only making our lives harder.