I firmly believe that any dog should be comfortable and happy in a crate because they are necessary for certain things -- But I'm also of the camp that I don't think that the crate is a "babysitter" for when I'm just too lazy to watch my dog. Kaiser is only in a crate at night, in the car and when I'm doing agility with Luke (at trials & training).
Yes, puppy training can an exhausting and stressful time, but I figure it's what I signed up for. It's my job to watch Kaiser for signs that he needs to go out and to keep him happy, exercised and TIRED (makes my life much easier 
).
I make the crate a happy place by providing treats almost every time they go in (EVERY time in the beginning stages). I left a stuffy & a chewie in Kaiser's home crate in the beginning, but now he tends to change them out on his own every now and then. I always leave the door open when it's not bedtime and he's free to go in and out as he pleases. Usually he chooses to sit in his crate and watch me while I get ready in the morning.
With Luke I used the crate at night for about the first year (leaving the door open for the latter part) -- I anticipate doing the same with Kaiser, although Kaiser's crate is much less obstructive and could easily stay in the room without being too much of a bother.
Kaiser cried slightly the first night, but I just hung my hand over the bed and stuck my fingers through the crate and he's been fine ever since. We have a few crying issues at trials/training, but I just leave him to cry it out and he hushes after about 10 minutes. Each time it gets better, so I'm figuring it won't be an issue much longer. As with all training, crate training just takes time.
Luke -- Lab/Shepherd (1-1-04) Open Versatility, EAC, EJC, TN-E, TG-E, HP-O
Kaiser -- Alaskan Klee Kai (12-30-07) Future Agility Star!