This is because in order to heal or revive a dead pokemon one must give it to the pokecenter (in towns) or sleep. But sleeping is not an option, since one needs wool, and mareeps are not that common.
In order to solve that i think it would be a nice idea to be able to give food to the pokemons so they would slowly regenerate health while not on a pokeball.
It could also be a feature to make a pokemon sleep in order to revive or to fully recover all the health left.
This last thing could be done by putting a pokemon out of the pokeball and telling it to sleep via a keyboard key. The pokemon would remain in place and could not be able to battle. Of course this feature would mean that a sleeping animation have to be done for every pokemon.
It would mean a lot of work, but i think it would be very worth and the overall gameplay would be highly improved