There's actually a well documented training technique used with pups called "crate training" which is highly effective. If you look into it, you'll start using your play pen a lot more

Its not mean, in fact if you do it correctly, you can see that they will respond a lot better in obedience and house training.

Of course it doesn't mean they are in there all day, but that they learn how to be left alone in their space. I used crate training with my lab when she was a puppy while I was studying dog behaviour and it was awesome.