1. If the pokemon did not want to battle for the trainer, it could
a. run away
b. attack the trainer
2. Pokemon are not the same as real world animals. They are generally more intelligent, and they are much tougher, as they survive being hit by all sorts of attacks that would be fatal to humans or animals.
3. I can only speculate what goes on inside pokeballs, but Im confident its not like being in a room staring at a wall for days. In other words, it seems like biological processes are paused. They don't feel time passing, they don't heal or get worse without immediate care, they don't starve or grow.
The pokemon are not resisting the capture within a pokeball because they dont want the trainer to catch it. Because while they do resist the pokeball, they don't even attempt to flee (except for roamers...).
Resisting the pokeball is part of checking if the trainer is worth it.
The pokemon has 2 possibilities when meeting a trainer that might try to catch it:
-it can remain wild, surviving on its own, searching for food, shelter..
-being caught by the trainer, which assures its safety, and enables it to grow stronger