Their crate IS a good thing, like their bedroom. It's got their bed, food and water and toys in it.
What's not to like? Closing the door is just allowing your pup some quiet time, that's all. If you never treat it like punishment, believe me, your pup will never look at it that way.
Dogs by nature are den animals and feel comfortable to have a small space of their own.
An xpen is an exercise pen. You can google for them. Like this:
Pet Yard XT Pet Gate Enclosure
As for the whining, once he learns that whining does NOT get him attention, he will no longer do it. It took my puppy (at 11 weeks old) only one week to stop all barking/whining when left in his crate or alone at night. Now he thinks nothing of it.
As for leaving him alone, puppies sleep a lot and he will be having his meals and drinks in the crate, naptime in the crate and if you put chew toys in there he'll have something to keep him busy when he's awake. So he'll really want for nothing. In fact, if you don't want to leave him "alone" keep the pen and his crate in the same room you are most often in. It isn't about closing him up or isolating him, its about getting him to naturally hold his bladder (because he's in his den).
If you get the book "How to Housebreak Your Dog in 7 Days" this is basically her method, modified for puppies under 16 weeks. Once they reach 16 weeks she suggests feeding and watering on a strict schedule to aid in the training and get the dog on schedule. She says that about seven days is all a dog should need to get the hang of the schedule and the right potty area vs. the wrong.
I completely understand that you have reservations about crate training - my husband did as well at first. He felt like we were "locking him up". Truth is, we enjoy him much more now that he's crate trained because rather than having to follow him around every moment of the day/night OR just stumble upon accidents all over the house, we can relax and focus on him during his playtimes and know that he is safe and happy in his "room" when he's crated. His crate and pen are in the kitchen, with his crate (the open wire kind) right in the doorway, so he can constantly see/hear us in the main living area and going in and coming out of the kitchen.
And like I said, besides the first week we got him when he barked and whined at night and sometimes when left alone, now he never says a peep about it. He's the happiest pup around!