I think you're talking about world dynamics, anything that makes the world feel more alive and feel ever-changing. Pokemon and your examples are examples of world dynamics. I like world dynamics, but I find that it really depends on how and why certain dynamics are implemented. In the pokemon example, a better decision would have been to make all pokemon available at all times of day. The only difference is that some would be rarer depending on the time, and when found they would be asleep until attacked. That adds dynamics in its true form, without taking inconvenience beyond conceivable limits.
I don't mind inconvenience, but i want it to be tasteful and logical. Mud frogs come out in the rain? Fine that sounds awesome. But *only* found in the rain? No way. Mud Frogs don't just disappear from the face of the planet when it isn't raining. They come out in the open when its raining, but where are they when its not raining? They have to be somewhere. That means SE has to make them available; otherwise its just a needlessly inconvenient mechanic.
I prefer world dynamics, but only when it isn't done purely at the player's expense.
